qid int64 2 112k | question stringlengths 61 6.7k | positives listlengths 1 1 | negatives listlengths 1 10 |
|---|---|---|---|
2,937 | <p>Why are insects so energy-efficient while flying? Is it because of their light weight and aerodynamics or due to very efficient biochemical transformations (food->energy)?</p>
| [
{
"answer_id": 2960,
"pm_score": 5,
"text": "<p>Insect flight muscle is capable of achieving the highest metabolic rate of all animal tissues, and this tissue may be considered an exquisite example of biochemical adaptation.</p>\n\n<p>Locusts, for example, may (almost instantaneously) increase their oxy... | [
{
"answer_id": 2939,
"pm_score": 3,
"text": "<p>The smaller an animal is the easier it becomes for it to fly. That is because surface area increases to the second power of the diameter of the animal whereas mass increases to the third. So the larger a thing is the more mass per surface are it has.</p>\n... |
2,942 | <p>The Murchison meteorite is an important piece of evidence for abiogenesis, because it contained nucleobases from extraterrestrial origin, as <a href="http://en.wikipedia.org/wiki/Murchison_meteorite">this Wikipedia article</a> explains.</p>
<blockquote>
<p>These results demonstrate that many organic compounds which are components of life on Earth, were already present in the early solar system and may have played a key role in life's origin.</p>
</blockquote>
<p>My question is: <strong>How did these nucleobases arise? Is it possible for these nucleobases to have been synthesized naturally from simpler molecules in a specific environment, like in the Miller-Urey experiment for amino acids?</strong></p>
| [
{
"answer_id": 2950,
"pm_score": 4,
"text": "<p>It is interesting to note that, in the Wikipedia article, it states that </p>\n\n<blockquote>\n <p>The amino acids were racemic (that is, the chirality of their enantiomers are equally left- and right-handed), indicating that they are not present due to t... | [
{
"answer_id": 2948,
"pm_score": 3,
"text": "<p>I think it's fair to say that we don't really know how these more complex organic molecules formed abiotically, but we can say that carbonaceous chondrites - a class of carbon and organic molecule bearing meteorites to which Murchison belongs (specifically... |
2,976 | <p>A reflex is an unconscious action in response to some specific stimulus, e.g., blinking an eye, or pulling the hand away from a hot pin</p>
<p>I know from school biology, and reading online that withdrawal reflexes are quick because</p>
<ul>
<li>CNS is involved</li>
<li>Danger receptors send impulses to prevent inhibition of flexion</li>
</ul>
<p>When a person is extremely obese, do these flexion impulses take longer? </p>
<p>Is a withdrawal reflex in an obese person noticeably slower than in case of a reasonably fit person? </p>
| [
{
"answer_id": 2994,
"pm_score": 2,
"text": "<p>No, what would weight have to do it? An obese person has more fat than a person of a normal weight, but fat isn't innervated by nerves (or motor neurons, at least). What about very muscular people? In this case, they actually have more muscles that require... | [
{
"answer_id": 3046,
"pm_score": 2,
"text": "<p>I went into this with the same assumptions that <code>jello</code> did, but I found two studies that had some interesting results.</p>\n\n<p><a href=\"http://www.ncbi.nlm.nih.gov/pubmed/20019633\" rel=\"nofollow\">Isojärvi (2010)</a> found that in obese an... |
2,977 | <p>I was reading through the <a href="http://www.cell.com/abstract/S0092-8674(12)00776-3" rel="nofollow noreferrer">Karr et al. (2012)</a> whole-cell computational model. One of the things they did was to induce single-gene disruptions in their model. They observed several to be fatal, but:</p>
<blockquote>
<p>In some cases (Figure 6B, fifth column), the time required for the levels of specific proteins to fall to lethal levels was greater than one generation (Figures 6C and 6D).</p>
</blockquote>
<p>As far as I understand this is because when a single-cell divides, daughters get not only get a copy of the mother DNA, but also have their initial levels of proteins and RNA set to those of their mother (or similar, with some statistical fluctuation).</p>
<p>To me this screams of <a href="http://en.wikipedia.org/wiki/Lamarckism" rel="nofollow noreferrer">Lamarkism</a>: if an organism during its lifetime came in contact with an environment that caused a greater expression of some protein that in had at birth, its children will also have a higher initial expression of the same protein. In other words, the trait of "level of this protein" seems to be being passed down in a Lamarkian way. <strong>Is my understanding correct, or am I missing the point?</strong></p>
<p>If my understanding is correct, then <strong>what are some standard methods to account for this short-term Lamarkism in mathematical models of evolution?</strong></p>
<hr />
<h3>Notes</h3>
<ul>
<li><p>I am primarily <strong>interested in mathematical (or other formal) treatments</strong> of this. I have a background in mathematics and some work in mathematical modeling for population biology and evolutionary game theory. I have <strong>no background in biochemistry or microbiology</strong>. I would appreciate answers or references that cater to this awkward background but I am not adverse to plowing through some microbio if it is for something awesome.</p>
</li>
<li><p>Similar partial arguments can be made for non-single-cell and sexual organism by considering hormone expressions of the mother during pregnancy, as <a href="https://biology.stackexchange.com/a/2876/500">in this answer</a>. I am satisfied with an explanation for asexual single-cell organisms, but bonus points if it can also say something about non-single-cell and/or sexual organisms.</p>
</li>
<li><p>Follow up question on modeling the mechanism behind this: <a href="https://biology.stackexchange.com/q/3020/500">Macromolecule levels in daughter cells after fission</a></p>
</li>
</ul>
| [
{
"answer_id": 4991,
"pm_score": 2,
"text": "<p>This phenomenon is well known and can be observed in several species. In fact, if you look at the time it takes for E. coli to change its transcription program in order to react to the environment (signal->transcription->translation), you will find it can ... | [
{
"answer_id": 4961,
"pm_score": 0,
"text": "<p>I would say not, though you might find occasional cases where it is important. </p>\n\n<p>Lamarckism could certainly apply to single celled organisms, but it would still tend to be associated with DNA. As originally described by Lamarck, the traits cited ... |
2,979 | <p>Hard water is water with high mineral/salt content. I'm told that a potted plant watered with a salt solution dries out sooner or later. Is this true? </p>
<p>If so, would a plant survive if watered using hard-water? </p>
| [
{
"answer_id": 4991,
"pm_score": 2,
"text": "<p>This phenomenon is well known and can be observed in several species. In fact, if you look at the time it takes for E. coli to change its transcription program in order to react to the environment (signal->transcription->translation), you will find it can ... | [
{
"answer_id": 4961,
"pm_score": 0,
"text": "<p>I would say not, though you might find occasional cases where it is important. </p>\n\n<p>Lamarckism could certainly apply to single celled organisms, but it would still tend to be associated with DNA. As originally described by Lamarck, the traits cited ... |
2,991 | <p>I have been tasked with writing a program for computing properties of a give set of peptides. These peptides are given as 1-letter amino acid sequences and I need to compute the following :</p>
<ul>
<li>Length of peptide</li>
<li>Number of Each Amino Acid</li>
<li>Percent composition of each amino acid</li>
<li>Molecular weight</li>
<li>Net charge of peptide </li>
<li>Positive charge </li>
<li>Negative charge</li>
<li>Isoelectric point (pI) </li>
<li>Hydropathicity</li>
<li>Percent polar amino acids </li>
<li>Percent positive amino acids </li>
<li>Percent negative amino acids </li>
<li>Percent hydrophobic amino acids </li>
<li><a href="http://en.wikipedia.org/wiki/Hydrophobicity_scales">Hydrophobicity</a> </li>
<li><a href="http://en.wikipedia.org/wiki/Lipophilicity">Lipophilicity</a></li>
<li>Amphiphilicity</li>
<li>Water-Octanol Partition Coefficient</li>
<li>Steric Bulk</li>
<li>Side chain bulk</li>
<li>Net donated hydrogen bonds</li>
<li>Percent \alpha helix</li>
<li>Percent random coil</li>
<li>Percent \beta sheet</li>
</ul>
<p>While some of these properties are self explanatory ( eg. size, num. of amino acids, percentage of amino acids. ) and easy to compute. Other properties ( like Molecular weight, Net. charge, Positive charge, Hydorphobicity etc ) have been difficult for me.</p>
<p>I donot have Chemistry or Biology background and hence have found these difficult to compute. I would be appreciative if someone could point me in the correct direction ( I have already been through Wikipedia ) containing methods to compute the above mentioned properties or to a standard text which would explain the above mentioned properties and also provide methods to compute them. Thank you all.</p>
| [
{
"answer_id": 2993,
"pm_score": 4,
"text": "<p>Biopython and the other bio-programming languages typically have examples of how to do this kind of thing. </p>\n\n<p>For example here is some python code for calculating some of these:</p>\n\n<p><a href=\"http://biopython.org/w/index.php?title=ProtParam&a... | [
{
"answer_id": 2992,
"pm_score": 3,
"text": "<p>That's quite a laundry list, and I doubt someone is going to sit down and give you hints for all of them. Note that some of the properties (like percent alpha helix) rely on prediction method (secondary structure prediction, in this case). \"Net donated hy... |
3,030 | <p>I'm interested in learning more about the biological systems or hormones or parts of the brain that affect short term (<15 minutes) ability to concentrate attention on the task and be aware of the situation.</p>
<p><strong>I'm particularly interested in humans who are engaged in an activity that can be perceived as threatening:</strong> martial arts, competitive video games, sports and other activities which may be considered "fight or flight", but a scenario in which the person has chosen to stay and fight. </p>
<p>To clarify the question further: <strong>What is involved in the ability to make decisions based on the competitive situation itself, instead of responding with pre-learned techniques and tactics?</strong> In one case, a person may be aware of what his/her opponents are doing, while in other cases the same person may "rush in blindly" and attempt to execute techniques that were learned and worked before, but will not work in the current situation. </p>
<p>What influences this choice of responding versus acting on prior knowledge?</p>
| [
{
"answer_id": 5098,
"pm_score": 2,
"text": "<p>thinking and decision making under stress or pressure is significantly reduced. its sometimes called the 'fight or flight' condition. </p>\n\n<p>This is a pretty well established phenomenon. Here's a great <a href=\"http://www.radiolab.org/2007/apr/09/gr... | [
{
"answer_id": 5093,
"pm_score": 0,
"text": "<p>I recalled a while ago that I saw a presentation on the concept of \"<a href=\"http://en.wikipedia.org/wiki/Flow_%28psychology%29\" rel=\"nofollow noreferrer\">Flow</a>\". </p>\n\n<p>Here's an overview by the author :<a href=\"http://www.ted.com/talks/miha... |
3,066 | <p>What is the difference between a naive p-value and an adjusted p-value in the results of a GWAS study? See from <a href="http://www.nature.com/ng/journal/v44/n8/full/ng.2344.html">this paper</a>:</p>
<blockquote>
<p>After Bonferroni adjustment, a single gene, DCTN4 (encoding dynactin 4) on chromosome 5q33.1, was significantly associated with time to chronic P. aeruginosa infection (naïve P = 2.2 × 10−6; adjusted P = 0.025; Supplementary Fig. 1).</p>
</blockquote>
| [
{
"answer_id": 3070,
"pm_score": 5,
"text": "<p>There’s an XKCD comic which <a href=\"http://xkcd.com/882/\" rel=\"nofollow\">explains the problem</a>. Unfortunately, that comic is too big to post here. Briefly, a <em>p</em>-value of 0.1 says (roughly) that there’s a 10% chance (0.1) of the observed res... | [
{
"answer_id": 3143,
"pm_score": 2,
"text": "<p>I'd argue this actually belongs on CrossValidated.</p>\n\n<p>Essentially, the problem is one of how a GWAS study is conducted. By looking over an entire genome for associations, you're actually conducting thousands or millions of experiments, not the singl... |
3,135 | <p>Is there a computer program that simulates biology on a molecular level? Software that has rules that simulates the rules of molecular-biology?</p>
| [
{
"answer_id": 3137,
"pm_score": 5,
"text": "<p>There is a recent paper that introduced the first molecular-level whole-cell simulation.</p>\n\n<p>Karr, J.R., Sanghvi, J.C., Macklin, D.N., Gutschow, M.V., Jacobs, J.M., Bolival, B., Assad-Garcia, N., Glass, J.I., & Covert, M.W. (2012). <a href=\"http... | [
{
"answer_id": 41739,
"pm_score": 2,
"text": "<p>NAMD is a molecular simulation software system with an extensive, active community of researchers</p>\n\n<p><a href=\"https://www-s.ks.uiuc.edu/Research/namd/\" rel=\"nofollow\">https://www-s.ks.uiuc.edu/Research/namd/</a></p>\n\n<p>it has a slick visuali... |
3,147 | <p>We work with a membrane protein system where measuring the affinity between the enzyme and the upstream activating protein has been difficult, and when measured in detergent solution, it is almost 100 fold lesser (ie ~100nM) whereas the EC50 in an enzymatic assay using vesicles in ~1-2nM. Would it be reasonable to say that the "real" affinity is ~1nM than 100s of nM based on the biochemical assay?</p>
<p>Alternately, is there a documented system where a huge discrepancy exists between measurements from direct binding and biochemical assays?</p>
| [
{
"answer_id": 3150,
"pm_score": 4,
"text": "<p>You can certainly get massive differences between EC<sub>50</sub> and affinity. This is especially true for cell-based assays and membrane protein systems. </p>\n\n<p>The reason why is because the appropriate time scales to achieve binding equilibrium (hrs... | [
{
"answer_id": 3250,
"pm_score": 3,
"text": "<p>In what follows I am going to attempt to answer your question using a specific example of (competitive) reversible activation, and I hope to show what a misleading parameter EC<sub>50</sub> can be. (Rate law derivation is an area of interest, hence the l... |
3,160 | <p>There doesn't seem to be a lot of information available on research done on warts. What is the life cycle of a wart? How does it spread? -- specifically how does it recruit cells to spread it? What is the life cycle of a PV-infected dermal cell? </p>
| [
{
"answer_id": 3162,
"pm_score": 4,
"text": "<p><a href=\"http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0365-05962011000200014&lng=en&nrm=iso&tlng=en\">This</a> article has some good information. It's certainly more than I want to know about warts.</p>\n\n<blockquote>\n <p>Iso... | [
{
"answer_id": 3175,
"pm_score": 2,
"text": "<p>Conner's response contained just the type of source material I was looking for. Thanks Conner -- let us all +1 him. Allow me to summarize the specifics of the <a href=\"http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0365-05962011000200014&am... |
3,227 | <p>I have just read <a href="http://www.guardian.co.uk/science/2012/aug/18/edward-wilson-harvard-biologist-interview">this article on E. O. Wilson</a> and I don't understand what the difference is between what he is arguing and "standard" natural selection.</p>
<p>I read "the extended phenotype" some years ago and from what I vaguely remember that argued that everything about selection comes down to genes: they are the units of what is inherited and drive everything else (and their reach can be quite surprising). At first glance that seems inconsistent with the article, since it mentions "group selection". But when you read the details it includes things like</p>
<blockquote>
<p>Group selection begins when a colony of creatures develops a behaviour
that gives it a competitive advantage over other groups. Initially,
this could be down to a <strong>random genetic mutation</strong>.</p>
</blockquote>
<p>which sounds like it's gene-based too (and examples seem to come from ants and the like which I thought were closely genetically-related across a colony too...).</p>
<p>So what is the fuss about? And how will it be resolved?</p>
<p>Maybe the difference is easier to explain in terms of some difference between mathematical models? If so, that's fine (I hope - it might make more sense than jargon in a field I am unfamiliar with ;o).</p>
<p>[Is this too "general public" for this site? Apologies if so.]</p>
| [
{
"answer_id": 3232,
"pm_score": 4,
"text": "<p>After reading the article, the fuss is about this:</p>\n\n<p>In currently accepted theory Eusociality or \"kin selection\" explains altruistic behavior (the sacrifice of yourself or resources you control for the betterment of something else besides you) by... | [
{
"answer_id": 3426,
"pm_score": 2,
"text": "<blockquote>\n <p>So what is the fuss about?</p>\n</blockquote>\n\n<p>The fuss isn’t so much about biology as it is about the circumstances of the argument. in particular, I gather that there are two complaints people have with E. O. Wilson’s (and his collab... |
3,246 | <p>I know that there are two most important directions of genetic information transfer in living organisms: DNA->DNA and DNA->RNA. The first is replication, and the second is transcription. I wonder if there is a reason for this choice of directions. According to <a href="http://en.wikipedia.org/wiki/Central_dogma_of_molecular_biology#General_transfers_of_biological_sequential_information" rel="nofollow">this article</a>, all other directions are possible. Why do we use DNA for example? RNA is capable of self-replication since it happens in viruses. And why do we use RNA, not DNA, as messenger molecules? Is it just an accident or is it possible to explain why this is the right way of doing it?</p>
| [
{
"answer_id": 3248,
"pm_score": 4,
"text": "<p>DNA is <a href=\"http://en.wikipedia.org/wiki/RNA#Comparison_with_DNA\">more chemically stable</a> than RNA, which makes it ideal for long-term storage. RNA viruses like HIV have a short lifespan and must replicate to survive, which is why they can get by ... | [
{
"answer_id": 3303,
"pm_score": 2,
"text": "<p>If you had a complex life form which used only DNA or RNA, it would have no way to tell transcribed mXNA from genomic gXNA. This would cause problems during cellar replication, as you could also replicate your mXNA along with your gXNA. It would also cause... |
3,247 | <p>In the past, when there was no pasteurization, could making yogurt from milk lower the chance of getting infected by bovine tuberculosis (or other diseases from infected milk)?</p>
<p>For example, would yogurt cultures reduce the amount of "bad" bacteria or create a less hospitable environment for them?</p>
| [
{
"answer_id": 3251,
"pm_score": 3,
"text": "<p>In short, 'No.'</p>\n\n<p>Yogurt, in and of itself, is the product of milk with specific strains of bacteria that are not particularly unique. Yogurt is just as hospitable to harmful bacteria as beneficial bacteria.</p>\n\n<p>The two mechanisms which sprin... | [
{
"answer_id": 3294,
"pm_score": 1,
"text": "<p>There have been studies regarding whether or not the bacterial load in yogurt (which would be the \"Live and active cultures\" part of yogurt - or the part where Jamie Lee Curtis talks about how you'll go back to pooping on schedule) helps protect the gut ... |
3,279 | <p>Typically when proteins aggregate, they will get stuck at the top of the well. However, we're seeing some protein aggregate in the stacking layer even when we're treating the loading volume with DTT.</p>
<p>One peculiar attribute of this experiment is that we're trying to carry out a Cu(I) catalyzed Azide-Alkyne Click rxn. Without the Cu(I), the proteins run normally. However, after Click rxn, we do see some of our expected clicked product, one of our proteins is disappearing into the top band. Hypothesis is that either the copper(I) is changing the migration or oxidative damage from the Cu(I)-> Cu(II) transition is altering the protein.</p>
<p>Returning to the original question, what would cause a protein to stop at the stacking layer vs. at the combs?</p>
<p>[edit]
According to my labmate who was having this problem, the protein was crosslinking with itself to create fairly sizeable polymers. We also saw ladders of the protein with ascending size. Spinning the clicked reaction removed the issue but also resulted at a lost of the protein. It sounds like he wasn't treating with a sufficient amount of DTT to break up the mixture.</p>
<p>This unfortunately still doesn't differentiate between proteins stuck at the combs vs stuck at the stacking layer.</p>
| [
{
"answer_id": 3284,
"pm_score": 3,
"text": "<p>Sounds like the copper cross linking the protein or creating aggregates that the SDS buffer can't break up. add EDTA to your loading buffer before you cook it? </p>\n"
}
] | [
{
"answer_id": 3312,
"pm_score": 2,
"text": "<p>At the interface of the stack gel and resolving gel is a pH change and a change in gel density. If you feel certain that your protein is not crosslinking so much that it can not enter the gel than I would think about the pH of the sample and the effect of... |
3,297 | <p>I read somewhere that a mature neuron loses its ability to divide, except for very specific situations. I was unable to find the description of those situations. What are they?</p>
<p>(I'm sorry I'm not saying where I read that, but I simply can't find it.)</p>
| [
{
"answer_id": 3298,
"pm_score": 4,
"text": "<p>Mature, differentiated neurons do not divide (undergo mitosis), but apparently there is a small population of self-renewing <a href=\"http://www.ncbi.nlm.nih.gov/books/NBK10920/\" rel=\"nofollow\">neural stem cells</a> in adults that can produce new neuron... | [
{
"answer_id": 3555,
"pm_score": 2,
"text": "<p>As was pointed out by @jello differentiated neurons do not divide, instead new neurons are recruited into existing networks from undifferentiated cells. This process is called neurogenesis. A high level summary of <a href=\"http://www.scholarpedia.org/arti... |
3,308 | <p>At school we were told on scale of 0 through 1000 the animal kingdom ranges from amoeba the simplest/primitive being at 0, and Humans the most complex animals at 1000; what are the equivalent complexity species (?) in the plant kingdom? What is the least complex plant, and the most complex?</p>
| [
{
"answer_id": 3309,
"pm_score": 5,
"text": "<p>That whole thing of being more complex is non-sense, you can't say that for animals and you can't say that for plants either. It all depends on how you look at it. Average number of cells? Size of genome? Size of the proteome? Adaptability to different env... | [
{
"answer_id": 3330,
"pm_score": 0,
"text": "<p>The venus fly trap would certainly appear one of the most complex plants.\nThe plant almost 'bridges' a lifeform gap.</p>\n"
}
] |
3,319 | <p>I asked a <a href="https://biology.stackexchange.com/q/3315/1308">question</a> related to the third sex, and I came to know that its always possible to categorize a human to male or female with presence of Y chromosome.</p>
<p>Now, I have another question. Is there a way to say if someone has Y chromosome <strong>only with external physical test</strong>? More specifically:</p>
<ul>
<li>Someone has a penis, can we say that s/he will have Y chromosome?</li>
<li>Some one has Y chromosome, can we say that he will have a penis?</li>
</ul>
| [
{
"answer_id": 3322,
"pm_score": 4,
"text": "<p>No, an external physical examination would be inconclusive. The reason is the TDF\ngene. To be more specific, if a person has XY and the gene is not active then the subject\nwould have a female appearance. Also we cannot conclude that a person has a Y\nchr... | [
{
"answer_id": 3336,
"pm_score": 2,
"text": "<p>An interesting condition is <a href=\"http://en.wikipedia.org/wiki/Androgen_insensitivity_syndrome\" rel=\"nofollow\">androgen insentivity syndrome</a>. In AIS, the body is unable to respond to androgens, the male sex hormone, of which testosterone is the ... |
3,356 | <p>I'm not versed in either biology or linguistics so please forgive any naiveties I may commit.</p>
<p>I've learned that Noam Chomsky thinks that language is a result of a single genetic mutation in humans. It would be a mutation allowing the human brain to conceive of natural numbers as I understand. Have there been any (even speculative) attempts by biologists to locate that mutation in the human genome and/or in time? Is it even feasible?</p>
| [
{
"answer_id": 3653,
"pm_score": 3,
"text": "<p>The anthropologist <a href=\"http://en.wikipedia.org/wiki/Svante_P%C3%A4%C3%A4bo#Work\" rel=\"nofollow\">Svante Pääbo</a> is more recently famous for trying to track down the 'language gene'. There isn't a lot of reference to Chomsky in his work as I've n... | [
{
"answer_id": 100919,
"pm_score": 2,
"text": "<p>To my knowledge, Chomsky does not claim that there is a specific gene or mutation responsible for the human linguistic abilities - at least not in strictly biological sense. The claims of Chomsky and his followers, known as <a href=\"https://en.wikipedia... |
3,379 | <p>A healthy immune response to a bacterial infection includes "memory" to permit the body to thwart subsequent exposure to same bacteria. What are the dynamics of using antibiotics on initial exposure to the bacteria regarding a possible degradation of the quality of this "memory" and thus the body's possibly compromised ability to fight a repeat exposure to same bacteria ?</p>
<p>I am not speaking of vaccines ... focus here is on bacteria </p>
| [
{
"answer_id": 3383,
"pm_score": 4,
"text": "<p>A quick search on ISI Web of Knowledge yielded this paper:</p>\n\n<blockquote>\n <p>R J North, P A Berche and M F Newborg (1981) Immunologic consequences of antibiotic-induced abridgement of bacterial infection: effect on generation and loss of protective... | [
{
"answer_id": 3381,
"pm_score": 2,
"text": "<p>Edited for Clarity:</p>\n\n<p>In order to invoke a memory response or create a memory response, there <em>must</em> be interaction with the Adaptive Immune System (usually CD40+ \"Helper\" T-Cells), and the interaction <em>must</em> come in the form of a p... |
3,403 | <p>What are the different, <strong>high-level</strong>, <strong>disjunct</strong> (mutually exclusive at one particular point in time) programs or pathways along which a eukaryotic animal cell can follow? Examples of programs would include growth, cell division, senescence and quiescence. Are there programs that differ between cell types?</p>
<p>Any I'm missing? If so, references much appreciated.</p>
| [
{
"answer_id": 3522,
"pm_score": 1,
"text": "<p>I'm going to answer my own question with suggestions collected from the comments.</p>\n\n<p><strong>A multipotent stem cell:</strong></p>\n\n<ul>\n<li>Growth\n<ul>\n<li>Growth and clonal division</li>\n<li>Growth, division and differentiation</li>\n</ul></... | [
{
"answer_id": 3415,
"pm_score": 3,
"text": "<p>To see the width of your question, have a look at what the Gene Ontology considers a cellular process:</p>\n\n<p><a href=\"http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0009987#term=children\" rel=\"noreferrer\">http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0009987#... |
3,420 | <p>Below are two quotes from the CDC about Hantavirus:</p>
<blockquote>
<p>"Researchers believe that people may be able to get the virus if they
touch something that has been contaminated with rodent urine,
droppings, or saliva, and then touch their nose or mouth."</p>
</blockquote>
<p>and:</p>
<blockquote>
<p>"You cannot get the virus from touching or kissing a person who has HPS."</p>
</blockquote>
<p>This is hard to believe. So, since human saliva is not a problem, can you be contaminated
by human urine or human droppings? The only way for me to interpret this logically is to
say that this virus lives at the end of the digestive tract (for both rodents and humans)
and people can be kissed because they have much better hygiene than rodents. Is there a
better interpretation?</p>
<p>Also, is there a simple reason why Hantavirus leaves the mouth (moving to the end of the
digestive tract) of an infected animal, but influenza does not?</p>
| [
{
"answer_id": 3577,
"pm_score": 3,
"text": "<p>Viruses can have many different conditions necessary for transmission. Viruses which have membrane surface coats (like HIV ) need to be in water all the time to survive. Cold and flu viruses are more resilient and can survive on a <a href=\"http://www.ny... | [
{
"answer_id": 3421,
"pm_score": 0,
"text": "<p>This paper is referred to in the Wikipedia entry for hantavirus as an example of human-human transmission. It may discuss the reasons why transmission is not normally via this route.</p>\n<blockquote>\n<p>Martinez VP <em>et al</em>. (2005) Person-to-person... |
3,422 | <p>Mammals have lungs, so do marine mammals. Nevertheless some marine mammals seem to die rather quickly when they strand on a beach.</p>
<p>As they have lungs and can breath while on land, why do they die so quickly? Not being in water only restricts them from food.</p>
<p>Do they maybe try to get back into the water so rudely that they get hurt by rocks and/or break bones? Pressure difference doesn't seem to be a problem as they can jump out of the water as well.</p>
<p>I was wondering after reading <a href="http://www.dailymail.co.uk/news/article-2197167/It-like-aircraft-crash-Horror-sixteen-pilot-whales-die-mass-stranding-rescuers-battle-save-rest-pod.html" rel="nofollow">this article</a> on stranded pilot whales that got spot but died rather quickly after.</p>
| [
{
"answer_id": 3424,
"pm_score": 5,
"text": "<p>In the case of whales, I always thought that it was something to do with the fact that they rely upon buoyancy to support their weight and <a href=\"http://whale.wheelock.edu/archives/ask99/0532.html\">this</a> seems to support that view:</p>\n\n<blockquot... | [
{
"answer_id": 3423,
"pm_score": 0,
"text": "<p>That's not exactly true, you are generalizing. For example seals are marine mammals (that's a rather large non-official group I think) and they don't die so quickly.</p>\n\n<p>Anyway, breathing is not the only thing necessary for survival. If you leave a ... |
3,455 | <p>The DNA copying enzymes have a hard time working to the end of a chromosome. For circular chromosomes this is not a problem, since there is not a sharp 'end'. However, for a linear chromosome, without extra mechanisms in place, a bit of DNA is lost off the end of the chromosome after each replication. Because of this, eukaryotes have a <a href="http://en.wikipedia.org/wiki/Telomere" rel="noreferrer">telomere</a> to cap off their chromosomes.</p>
<p>In most cells of a mutli-cellular organism, this telomere is slowly worn away after each reproduction leading to <a href="http://en.wikipedia.org/wiki/Apoptosis" rel="noreferrer">apoptosis</a>. Cells that need to reproduce indefinitely such as germ and stem cells have to invest in extra mechanisms to replenish the telomere. For multi-cellular eukaryotes I can see how this might be usefull (for instance as a cancer counter mechanism). However, multi-cellular organisms evolved from single-cell eukaryotes.</p>
<p>I cannot see a reason for wanting apoptosis in a single-cell organism. However, single cell eukaryotes (say yeast) still have linear chromosomes with telomere caps. <strong>What advantage did linear chromosomes provide single-cell eukaryotes to offset the extra investment in reparing the telomere?</strong></p>
<hr />
<h3>Related questions</h3>
<ul>
<li><a href="https://biology.stackexchange.com/q/1090/500">What is the advantage of circular DNA in bacteria? </a></li>
</ul>
| [
{
"answer_id": 3459,
"pm_score": 4,
"text": "<p>I think it is the wrong question. You assume that eukaryotes developed from a single-cell organism with circular DNA. Then, clearly, there must have been an advantage of (newly) developing a linear genome. But eukaryotes could have developed from an organi... | [
{
"answer_id": 15752,
"pm_score": 1,
"text": "<p>I think its related to structure, like the noncoding (junk) DNA contributes to structure my guess would be that the Linear genome \"just happend\" and there was no way of going back.</p>\n\n<p>That could have been because of Phage/Viral predation radical ... |
3,465 | <p>As we have heard in the summaries of the human ENCODE project, <strong>80 per cent of junk DNA appears to have an essential function</strong>. Many fish have a genome with only one tenth the size of a usual vertebrate genome. Why can fish have 1/10th of junk DNA and be still fully functional? What has a frog more than a fish has? I'm especially interested if we can see the difference somewhere, complexity of physiology or anatomy, or such.</p>
<p>Jap. puffer fish genome: 390 Megabases, 47,800-49,000 genes (UniProt)</p>
<p>Medaka genome: 690 Megabases, 24,600 genes</p>
<p>Clawed frog: 1,500 Megabases, 23,500 genes</p>
| [
{
"answer_id": 3468,
"pm_score": 4,
"text": "<p>Genome size is a poor indicator of an organism's <em>complexity</em> (already an ill-defined term). We cannot assume by any means that a larger genome corresponds to a more \"complex\" organism. There are some plants whose genomes are larger than most mamm... | [
{
"answer_id": 3467,
"pm_score": 3,
"text": "<p>See <a href=\"http://genomeinformatician.blogspot.co.uk/2012/09/encode-my-own-thoughts.html\">here</a> for an ENCODE author's reflections on their use of the word \"functional\". (I don't think anyone is using the word \"essential\".)</p>\n\n<p>It is clear... |
3,476 | <p>The mushrooms are gilled with a light-brown cap. The stem is widened to the base.</p>
<p>What species is it? Is it considered edible?</p>
<p>They are found in mixed forest in Moscow, Russia. They grow in the ground quite separated from each other.</p>
<p><img src="https://i.stack.imgur.com/0zzZ8.jpg" alt="enter image description here"></p>
| [
{
"answer_id": 3468,
"pm_score": 4,
"text": "<p>Genome size is a poor indicator of an organism's <em>complexity</em> (already an ill-defined term). We cannot assume by any means that a larger genome corresponds to a more \"complex\" organism. There are some plants whose genomes are larger than most mamm... | [
{
"answer_id": 3467,
"pm_score": 3,
"text": "<p>See <a href=\"http://genomeinformatician.blogspot.co.uk/2012/09/encode-my-own-thoughts.html\">here</a> for an ENCODE author's reflections on their use of the word \"functional\". (I don't think anyone is using the word \"essential\".)</p>\n\n<p>It is clear... |
3,481 | <p>Here's the reason why I'm asking: I've heard that it takes some time for pets(cats/dogs) to adjust to a different dry feed, where the new feed has to be mixed with the old one, slowly replacing the old one. I'm wandering if this advice has any truth in it, and if so, does this apply to humans as well?</p>
<p>For example, a cat eats the same kind of food for months at a time, but humans vary their diet much more dramatically. <strong>Are there any benefits to eating the same kind of food over extended period of time?</strong> I'm interested in knowing if the digestive system/symbiotic bacteria in the gut adapts to the food, resulting in better digestion/absorption of nutrients.</p>
<p>Thank you for your input!</p>
| [
{
"answer_id": 5046,
"pm_score": 3,
"text": "<p>I think it would depend on the benefits you are looking for.</p>\n\n<p>If you ate the same thing everyday, it's possible your intestinal flora, and the rest of your GI tract would optimize themselves for maximal nutritional extraction. It is known that the... | [
{
"answer_id": 8090,
"pm_score": 0,
"text": "<p>I've seen in a documentary that inuit, eating only seals for a longer period of time are some of the most healthy people on the planet.<br>\nHowever I can't seem to find that documentary anymore.</p>\n\n<p>I did found a wiki article about this subject:</p>... |
3,504 | <p>A few years back I heard at biology class that sugar's molecule consists of half the number of elements of a glucose molecule. So not counting the energy needed to transform two sugar molecules in one glucose molecule, isn't it almost the same (eating N amount of sugar) as eating N/2 of glucose?</p>
| [
{
"answer_id": 3506,
"pm_score": 4,
"text": "<p>You have it backwards. One sugar molecule is equivalent to <strong>two</strong> glucose molecules, though the actual structure of sugar (<em>Sucrose</em>) is a <em>Glucose</em> + <em>Fructose</em> combination.</p>\n\n<p>While Glucose is metabolized via Gly... | [
{
"answer_id": 3505,
"pm_score": 2,
"text": "<p><em><strong>Is consuming sugar with food as beneficial as consuming glucose (~half of the amount of sugar)?</em></strong></p>\n\n<p>What is referred to in everyday language as \"sugar\" is sucrose. Each sucrose molecule consists of one glucose molecule and... |
3,507 | <p><a href="https://en.wikipedia.org/wiki/Quorum_sensing" rel="nofollow noreferrer">Quorum sensing</a> is a system of stimulus and responses correlated to population density that is used by bacteria to coordinate gene-expression. I am looking for a simple computational/mathematical model of quorum sensing that abstracts away from the details of the mechanism implementing it inside the agent, but keeps the key inter-agent properties like diffusion rate, range, and timing.</p>
<p><strong>Is there a standard abstract mathematical model of quorum sensing used by biologists?</strong></p>
<p>I am not interested in the particulars of a specific organism, but would like a general model I could apply to capture the 'gist' for any organism that relies on quorum sensing for part of its behavior.</p>
<hr />
<p><a href="https://www.sciencedirect.com/science/article/pii/S0304397506007493" rel="nofollow noreferrer">Bernardini et al. (2007)</a> provided an extension to <a href="https://en.wikipedia.org/wiki/P_system" rel="nofollow noreferrer">P-systems</a> incorporating the basics of quorum sensing, and <a href="https://direct.mit.edu/artl/article-abstract/14/1/95/2599/A-Model-of-the-Quorum-Sensing-System-in-Vibrio" rel="nofollow noreferrer">Romero-Campero & Pérez-Jiménez (2008)</a> have used their approach to model bioluminosity in <em>vibrio fischeri</em>. This approach is conceptually appealing to me, but that is because I am predominantly a computer scientists. Although P-system can be used for modeling biological systems <a href="https://link.springer.com/article/10.1023/A:1024943605864?from=SL" rel="nofollow noreferrer">(Ardelean & Cavaliere, 2003)</a>, they still feel fundamentally computer-science-y and are typically not published in orthodox biological venues. This makes me suspect there is a more standard approach among biologists, probably via dynamic systems and diffusion equations.</p>
| [
{
"answer_id": 3517,
"pm_score": 3,
"text": "<p>I found <a href=\"http://dx.doi.org/10.1371/journal.pcbi.1002361\" rel=\"nofollow\">this paper<sup>[1]</sup></a>, which might be relevant; it uses is a more chemically inspired approach. <a href=\"http://dx.doi.org/10.1103/PhysRevE.84.041921\" rel=\"nofoll... | [
{
"answer_id": 107669,
"pm_score": 2,
"text": "<p>Since the accepted answer is nearly a decade old, I'm adding a new answer to address a recent piece of research that presents a good framework for modeling quorum sensing over small distances.<sup><strong>1</strong></sup></p>\n<p>First, the authors consi... |
3,510 | <p>According to <a href="http://dx.doi.org/10.1200/JCO.2009.25.5729">Korde et al.</a> (2010):</p>
<blockquote>
<p>Male breast cancer accounts for less than 1% of all cancers in men and less than 1% of breast cancers.</p>
</blockquote>
<p>This raises the question: <em>Why do most breast cancers occur in women?</em></p>
<p>Two plausible explanations I can think of:</p>
<ul>
<li><p>A male is less likely to get breast cancer for anatomical reasons (such as a smaller quantity of breast tissue, or breast tissue that is less susceptible to cancer),</p></li>
<li><p>Women have higher significantly levels of estrogen, which is linked to mutations that cause breast cancer (see <a href="http://dx.doi.org/10.1016/j.bbcan.2006.03.001">Cavalieria et al.</a> (2006)).</p></li>
</ul>
<p>Although, I have no evidence to suggest that either of these is predominant factor.</p>
| [
{
"answer_id": 3621,
"pm_score": 4,
"text": "<p>Yes, this is mostly about estrogen. Most breast cancers rely on endogenous estrogen to sustain proliferation.</p>\n\n<p>Some general reading: <a href=\"http://www.ncbi.nlm.nih.gov/books/NBK13155/\" rel=\"nofollow noreferrer\">Cancer Medicine, Chapter 18</a... | [
{
"answer_id": 15264,
"pm_score": 2,
"text": "<p>For two reasons: Women are</p>\n<ol>\n<li>exposed to estrogen,¹ and</li>\n<li>the lobules in a woman's breast go through 4 stages:</li>\n</ol>\n<p>Type 1: prepubescent & Type 2: pubescent</p>\n<p><img src=\"https://i.stack.imgur.com/fghqv.gif\" alt=\"... |
3,521 | <p>I read <a href="http://www.independent.co.uk/news/science/success-isnt-written-in-the-stars-its-in-the-length-of-your-fingers-1334251.html">this</a> article which has the following quote:</p>
<blockquote>
<p>The ratio between index and ring finger is believed to be linked to exposure to the male hormone testosterone in the womb.</p>
</blockquote>
<p>And I wonder what determines the amount of exposure to testosterone in the womb. Is it testosterone produced by the fetus itself, in which case the baby's own genetics is the answer, or does this exposure the article speaks of more likely refer to testosterone produced by the mother and exposed to the baby?</p>
| [
{
"answer_id": 3523,
"pm_score": 4,
"text": "<p>Fetal testis produces testosterone from cholesterol. There is a peak of production around 15 weeks of gestation (the \"masculinization programming window\"). So the genotype of the fetus can affect testosterone levels directly via effects on the biosynthes... | [
{
"answer_id": 70795,
"pm_score": 0,
"text": "<p>It has long been evident that human fetuses produce the hormones that dominate their development in utero. (Ref: <a href=\"https://www.ncbi.nlm.nih.gov/pubmed/144143\" rel=\"nofollow noreferrer\">Robinson et. al., J Clin Endocrinol Metab. 1977 Oct;45(4):... |
3,533 | <p>In a hospital I can see a long queue of pregnant women waiting for their turn for ultrasound. Is it safe to go through the ultrasound during pregnancy, especially during last few weeks?
Is ultrasound really required? What if it is not done? How does ultrasound affect baby?</p>
| [
{
"answer_id": 3535,
"pm_score": 4,
"text": "<p>As Luke points out, the ultrasound is very safe. However, in many cases it is not required. Typically by 20 weeks into the pregnancy, and sometimes earlier, a baby's sex can be determined by examining the genitals via ultrasound. My experience is that this... | [
{
"answer_id": 3534,
"pm_score": 3,
"text": "<p>The U.S. Food and Drug Administration (FDA) has the following information regarding the risks of ultrasound imaging;</p>\n<blockquote>\n<p>Ultrasound imaging has been used for over 20 years and has an excellent safety record. It is non-ionizing radiation, ... |
3,548 | <p>Here's <a href="http://theearlybirder.com/corvids/am-crow/pages/6002831%20American%20Crow.htm" rel="nofollow noreferrer">a picture</a> (by Rob Curtis) of a crow carrying and eating the corpse of what looks a bit like a small hawk or falcon:</p>
<p><img src="https://i.stack.imgur.com/TZ4p9.jpg" alt="Crow carrying dead bird"></p>
<p><a href="http://theearlybirder.com/corvids/am-crow/pages/6003000%20American%20Crow.htm" rel="nofollow noreferrer">Other</a> <a href="http://theearlybirder.com/corvids/am-crow/pages/6002847%20American%20Crow.htm" rel="nofollow noreferrer">pictures</a> clearly show the crow is eating the dead bird. <a href="http://theearlybirder.com/corvids/am-crow/pages/6002847%20American%20Crow.htm" rel="nofollow noreferrer">This image</a> shows the underside of the head and beak; <a href="http://theearlybirder.com/corvids/am-crow/pages/6002825%20American%20Crow.htm" rel="nofollow noreferrer">this one</a> shows its legs, which are grayish.</p>
<ol>
<li><strong>What bird is being eaten?</strong></li>
<li><strong>Is this bird a usual part of the corvid diet?</strong> Or did the crow just opportunistically scavenge a dead bird?</li>
</ol>
| [
{
"answer_id": 3550,
"pm_score": 5,
"text": "<p><a href=\"http://en.wikipedia.org/wiki/Crow#Diet\" rel=\"noreferrer\">Crows</a> are omnivorous, and will eat almost anything they find or can kill.</p>\n\n<p>In this case the prey looks like a <a href=\"http://en.wikipedia.org/wiki/Northern_flicker\" rel=\... | [
{
"answer_id": 101087,
"pm_score": 1,
"text": "<p>It's eating a flicker woodpecker. And yes, it did kill it and is eating it. Crows and ravens are omnivorous but also predators. They will opportunistically kill any small prey they can catch. Most birds are too quick for a crow, but flickers and all wood... |
3,564 | <p><a href="http://en.wikipedia.org/wiki/Antibody">Antibodies</a> have the ability of recognising highly specific peptide sequences and bind it at their antigen-binding site.</p>
<p>This ability is harnessed as a tool in research to purify target structures in the cell (e.g. in <a href="http://en.wikipedia.org/wiki/Chromatin_immunoprecipitation">chromatin immunoprecipitation</a>, ChIP).</p>
<p>Now let’s say that I’ve identified an interesting target structure (such as a particular transcription factor) and I want to design an antibody to use in ChIP against said target. How would I go about producing such an antibody, taking into account that it should be both highly sensitive and specific?</p>
| [
{
"answer_id": 5185,
"pm_score": 4,
"text": "<p>I worked for a long time at a leading high-quality antibody company, so I'll try and share some of my experiences with you. The process of making a highly specific antibody (I'll focus on monoclonals) has three important parts - antigen design and immuniza... | [
{
"answer_id": 5227,
"pm_score": 1,
"text": "<p>Answering Konrad's comment, you produce the peptide or protein of interest using bacteria or chemically synthesize them (chemical synthesis generally only work for short peptide chains. After which, you get a lot of side products). This peptide or protein ... |
3,585 | <p>If some time in the future, we can know exactly what a cell (for example simple prokaryote bacteria) contains, (I mean, exactly which molecules, the shape of them, the density of each, everything), Then can we create a new cell (not from another cell)?</p>
<p>I mean, if we have such technology, then create a soup just like what that cell contains, and a DNA exactly same as that bacteria cell, and then put some of it inside a Cell membrane, will it start living?</p>
| [
{
"answer_id": 3665,
"pm_score": 2,
"text": "<p>I think it could feasible to assemble complete synthetic cells in future. One of the first successes will probably be a simple bacteria. The synthetic genome is already on the road, so here, I'm pointing to other technologies that can be helpful. Feel free... | [
{
"answer_id": 7329,
"pm_score": 2,
"text": "<p>Many of the parts of a cell, which perform its basic functions, such as transcription, translation, DNA replication, etc. have been already isolated and successfully recreated in a test tube. So if we obtain a complete list of all the parts we need and kno... |
3,622 | <p>I was arguing with my colleague about this matter (I'm not going to mention which side I fall on).</p>
<p>Would death be immediate in the vacuum of space? For example, if I was suddenly teleported into the vacuum of space would I die straight away? Or would I experience a suffocating sensation?</p>
| [
{
"answer_id": 3623,
"pm_score": 5,
"text": "<p>Nope, you wouldn't die <em>instantly</em>. While explosive decompression has never been tested on humans (for obvious reasons), the dangers of a vacuum have mostly to do with the pressure differential between your body and the now pressure-less void around... | [
{
"answer_id": 80629,
"pm_score": -1,
"text": "<p>If an astronaut were teleported into space without her spacesuit/helmet, she would feel a suffocation feeling, likely making breathing motions even though there is no air to breathe. She would also feel her sweat, saliva, tears, mucous, and any other wa... |
3,659 | <p>Can female <em>Drosophila melanogaster</em> lay egg without males? </p>
<p>I maintain our lab stock but find a line that seems to have all females (or all males). The flies have been in the vial for two weeks, but I don't see any eggs hatching or become larva. </p>
| [
{
"answer_id": 5363,
"pm_score": 3,
"text": "<p>Yes, I regularly have to collect female virgins (12500 of them in the last week). They will lay eggs especially when there is extra yeast available. It is actually a good way to check virginity (in case a fly hatched early and was already mature, or a male... | [
{
"answer_id": 5362,
"pm_score": 2,
"text": "<p>Very old females (such as those in vials that have not been flipped for a long time) will often lay unfertilized eggs in the absence of males.\nThis happens to me occasionally when I am collecting virgins and then forget about them for a while.</p>\n"
}
... |
3,681 | <p>Reading a <a href="http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1001284">paper</a> about gene evolution, I see that they do phylogenetic analysis for bacteria using protein sequences. They take the method from <a href="http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.0030130">another paper</a>.</p>
<p>I can suspect that amino-acid sequences are more stable than nucleotide sequences, to the presence of synonymous substitutions.... but, is this stability required between closely related species? doesn't it make the analysis less powerful? does it make it more reliable? In other words, what's the advantage of using amino-acid sequences versus using nucleotide sequences for phylogenetic analysis?</p>
| [
{
"answer_id": 3683,
"pm_score": 4,
"text": "<p>In general, many sequence alignment programs can use multiple <a href=\"http://www.molecularevolution.org/resources/models\">substitution models</a>, distinguishing between nucleotides, amino acids, and codons. A protein sequence has functional information... | [
{
"answer_id": 3796,
"pm_score": 3,
"text": "<p>Due to the fact that several codons can code a same amino-acid, the amino-acid sequence is usually more conserved than the nucleotide sequence.</p>\n\n<p>For small scale studies, the higher variability of nucleotide data brings useful characters to establi... |
3,689 | <p>I've heard both ways; people going to the doctor for a cold and then getting a prescription for antibiotics and those that go to the doctor and told they have ride it out because <em>it's a viral infection</em>. Do antibiotics really help in true cases of a viral cold?</p>
| [
{
"answer_id": 3693,
"pm_score": 4,
"text": "<p>In general antibiotics don't help with viruses. However, sometimes a bacterial infection may follow a cold virus, so there might be some scenarios in which antibiotics would be needed. However in many cases it could be due to people demanding antibiotics f... | [
{
"answer_id": 17789,
"pm_score": -1,
"text": "<p>Antibiotics kill bacteria, not virus! So it's just plain wrong. If a bacterial infection appears after the cold, then the antibiotics should be prescribed because of the bacterial infection, not because of the cold. There is a serious concern about misus... |
3,696 | <p>There is plenty of anecdotal evidence ("<em>beer after wine and you'll feel fine, wine after beer will make you feel queer</em>") that mixing alcoholic drink types leads to a stronger effect, but I can't find any true studies. </p>
<p>In fact the only studies I found are looking at mixing energy drinks and alcohol (mixing with energy drinks increases motivation for more alcohol (in college students) [<a href="http://dx.doi.org/10.1111/j.1530-0277.2012.01868.x" rel="nofollow">1</a>]), and discussed mixing caffeinated beverages with alcoholic ones [<a href="http://www.ncbi.nlm.nih.gov/pubmed/22184486" rel="nofollow">2</a>].</p>
<p>Are there any studies specifically looking at mixing alcoholic drinks? They would have to compare people drinking the same amount of alcohol, but some people mixing, others drinking the same thing. Maybe even a cross-over study design? Same people do both, one after the other? The only way to get an unclouded answer!</p>
<p>I am also interested in the follow-up <em>why</em> question: Why does mixing some drinks make you more drunk? Presumably it is something in wine (for example) that interacts badly with something in beer at the chemical level (the metabolites maybe)?</p>
<ol>
<li>Marczinski CA, <em>et al</em>, (2012). Mixing an Energy Drink with an Alcoholic Beverage Increases Motivation for More Alcohol in College Students. <em>Alcohol Clin Exp Res</em>, epub. doi: <a href="http://dx.doi.org/10.1111/j.1530-0277.2012.01868.x" rel="nofollow">10.1111/j.1530-0277.2012.01868.x</a></li>
<li>Touyz LZ, (2011). Mixing drinks and concocting troubles. <em>Curr Oncology</em>, <strong>18</strong>(6):262-3. <a href="http://www.ncbi.nlm.nih.gov/pubmed/22184486" rel="nofollow">PubMed</a>; <a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3224025/" rel="nofollow">FullText</a>.</li>
</ol>
| [
{
"answer_id": 3698,
"pm_score": 5,
"text": "<p>There are some very general answers to your question.</p>\n<ol>\n<li><p>Definitely, there is a lot of magical thinking. We as humans are very prone to anecdotical evidence and extrapolations from incomplete data, even more so when we are drunk.</p>\n<p>As ... | [
{
"answer_id": 36067,
"pm_score": 0,
"text": "<p>Mixing of alcohol and energy drinks can be detrimental to ones health as both alcohol and the caffeine in energy drinks are both stimulants which can cause adverse effects on the heart especially if one has a natural sensitivity to caffeine. One also has... |
3,721 | <p>If I insert a new gene with a yeast integrating plasmid and select with a drop out culture once, can I assume that the newly integrated gene will stay in the strain without putting selective pressure on it? (i.e. can i use normal liquid culture and plates after getting the yeast with the newly integrated strain? </p>
| [
{
"answer_id": 3724,
"pm_score": 3,
"text": "<p>It depends upon exactly what you have done.</p>\n\n<p>The standard way of using a yeast intergrating plasmid (YIp) is for it to integrate into the genome by recombination between a piece of yeast DNA that the YIp carries and the same DNA in the genome. Thi... | [
{
"answer_id": 3725,
"pm_score": 2,
"text": "<p>Yeast integrating plasmids are known to be stable, even in absence of a selective medium but can revert like most homologous recombination plasmids. </p>\n\n<p>Quoting from the book <em>Yeast Gene Analysis (pg476)</em>:</p>\n\n<blockquote>\n <p>YIps are g... |
3,734 | <p>The potato appears to propagate by growing an 'eye'/'bud' which eventually grows into a new plant. So there would probably be single representative of the potato species in the world with all others being genetically identical. </p>
<p>Yet wikipedia indicates there are several closely related species of the potato; apparently as a result of selective breeding. To my understanding (which is probably wrong) there is only a single potato that grows the eyes without the need for a second parent - so there should probably only be the same genes repeated in each potato/plant. </p>
<p>What am I missing here? Why are there multiple varieties of the potato? </p>
| [
{
"answer_id": 3736,
"pm_score": 4,
"text": "<p>You're missing that potatoes also reproduce sexually. </p>\n\n<p>They're flowering plants, and they produce seeds that are not genetically identical to their parent plants. </p>\n"
}
] | [
{
"answer_id": 3761,
"pm_score": 2,
"text": "<p>Well, <strong>uvesten</strong> is correct in saying that potatoes are flowering plants and as such they can reproduce sexually. However, as <strong>everyone</strong> mentions potatoes can, like many plants, reproduce asexually by putting out clones.</p>\n\... |
3,741 | <p>I have been reading about Townes and Holtfreter's work in 1955, in which cells are dissociated from a blastocyst in an alkaline solution then mixed together and spontaneously reaggregates based on type, so epidermal cells around the outside and neural plate cells in the middle.</p>
<p>I understand enough about cell adhesion to understand why the cells will seem to attract cells of their own type, but would like to know how they can initially detect what to become and where they are needed in a specialised form, without something acting like a brain telling them what to become and where to go.</p>
<p>If the selection from the available types is random, as I suspect, what happens to blastocysts with too much epidermal tissue or vice versa? I'm struggling to imagine how organisms like this can develop without something taking the lead and actively coordinating what goes where.</p>
| [
{
"answer_id": 3744,
"pm_score": 4,
"text": "<p>Cell differentiation, cell fate and cell mapping is an interplay of accessible evolutionary strategies/programmes and responses to dynamic environmental cues such as specialized hormones (e.g. morphogens) and physical parameters and constraints. That is pu... | [
{
"answer_id": 3757,
"pm_score": 2,
"text": "<p>I would like to add to Lo Sauer's nice answer but give a slightly different perspective.</p>\n\n<p>What you referred to as the \"brain\" of the cell, is mostly its regulatory program. An abstract way to think about the regulatory program is like a computer... |
3,758 | <p>A few years back when I was reading The Selfish Gene by Richard Dawkins, there's this short passage where he theorizes about a way to achieve an increased lifespan through controlled evolution. </p>
<p>The theory goes like this: we don't tend to have medical problems until after 30 because we all tend to reproduce before that age. Thus, people who tended to die before 30 never passed on their dying-prone genes.</p>
<p>So, if you didn't let people reproduce before a age X (where X starts at 30) and then slowly move that age up, you could use evolution to increase lifespan.</p>
<p>The ethical issues notwithstanding, is there any reason why this wouldn't work? If it would work, how long do you think you would need to sit at each value of X? How far apart do you think each value could be? Finally, how many generations, using this technique, would it take before someone would live to be 1000 naturally?</p>
| [
{
"answer_id": 3759,
"pm_score": 5,
"text": "<p>I think this would probably work. The <a href=\"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2745839/\" rel=\"noreferrer\">grandmother effect</a>, which is one of the main theories for human longevity after fertility might indicate that human lifespan woul... | [
{
"answer_id": 51993,
"pm_score": 2,
"text": "<p>This <em>has been done</em> in fruit flies. At least two labs have used selection to breed longer-lived flies.</p>\n\n<p>Rose, M. <a href=\"https://www.jstor.org/stable/2408434?seq=1#page_scan_tab_contents\" rel=\"nofollow\">Laboratory Evolution of Postp... |
3,767 | <p>Is it right to assume that the first living organisms on earth had a linear genome? I base this on the fact that <em>linear</em> <strong>macromolecules</strong> <em>are clearly much more common in nature that circular ones</em>. To be honest, I can't even think of any naturally-occurring circular macromolecules that aren't already a part of current living organisms. </p>
<p><strong>Were the very first living organisms more likely to have linear genomes? If so, when during evolutionary time did circular chromosomes originate?</strong></p>
| [
{
"answer_id": 3759,
"pm_score": 5,
"text": "<p>I think this would probably work. The <a href=\"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2745839/\" rel=\"noreferrer\">grandmother effect</a>, which is one of the main theories for human longevity after fertility might indicate that human lifespan woul... | [
{
"answer_id": 51993,
"pm_score": 2,
"text": "<p>This <em>has been done</em> in fruit flies. At least two labs have used selection to breed longer-lived flies.</p>\n\n<p>Rose, M. <a href=\"https://www.jstor.org/stable/2408434?seq=1#page_scan_tab_contents\" rel=\"nofollow\">Laboratory Evolution of Postp... |
3,769 | <p>The electron transport chains of both the light reactions of photosynthesis (in plants) and oxidative phosphorylation (in animals) <em>both contain 5 complexes</em> including ATP synthase, as shown below.</p>
<p><img src="https://i.stack.imgur.com/2mXZt.png" alt="Oxidative phosphorylation">
<a href="http://prodomweb.univ-lyon1.fr/priam/REL_JUL03/RALSTO_ALL/PRIAM_REPLICON/RES_PRIAM/map00190_org.html" rel="noreferrer">Image Source</a></p>
<p><img src="https://i.stack.imgur.com/UuhZi.png" alt="Light Reaction">
<a href="http://en.wikipedia.org/wiki/File:Thylakoid_membrane.png" rel="noreferrer">Image Source</a></p>
<p>Is this coincidence, or does this possibly suggest that both chloroplast and mitochondrion precursors derived their energy-obtaining mechanisms via an ancient evolutionarily-related metabolic pathway which diverged?</p>
| [
{
"answer_id": 3795,
"pm_score": 4,
"text": "<p>Your latter assumption is the best we have so far, to my understanding.</p>\n<p>Here are a few excerpts from <a href=\"http://www.plantphysiol.org/content/154/2/434.full\" rel=\"noreferrer\">"Early Evolution of Photosynthesis"</a> published in <e... | [
{
"answer_id": 3792,
"pm_score": 1,
"text": "<p>Well, according to the <a href=\"http://en.wikipedia.org/wiki/Endosymbiotic_theory\" rel=\"nofollow\">endosymbiosis theory</a> both mitochondria and chloroplasts derive from ancestral bacteria that invaded/were phagocytosed (fancy word for eaten) by eukary... |
3,834 | <p>When I grew rabbits, I had a pair, one male and one female. And while the female's nipples were quite prominent, especially after giving birth, I don't remember the male having any nipples at all.</p>
<p>Do males of other mammal species, have nipples like human males, or is it a trait that's unique to Humans?</p>
| [
{
"answer_id": 3844,
"pm_score": 4,
"text": "<p>At the very least, I know that male primates also have nipples like female, though they are very close relatives to human. On the other hand, in some of my dissection labs, I noticed that male pigs also have nipples just like the female ones. It seems to b... | [
{
"answer_id": 20837,
"pm_score": 4,
"text": "<p>Most mammalian males have nipples. The duck-billed platypus does not have nipples but you begin to see development of nipples in marsupials (<a href=\"http://www.cabdirect.org/abstracts/20043175290.html;jsessionid=708CD968A3EA792683AF92AE0D2AE6C1\" rel=\"... |
3,871 | <p>I'm trying to represent data graphically and am using a variation of hue/lightness to distinguish one data point from the next. I would like to use a color that would allow me to convey most information visually.</p>
<p>What I'm interested in is which color I should use. <strong>I've read somewhere that humans are most capable of distinguishing shades of green, that is a human can differentiate more shades of green than any other color. Is it true?</strong> </p>
<p>Has there been any studies to distinguish the number of shades that a typical westerner can distinguish? I'm looking for information like : ### shades of green, ### shades of red, ### shades of cyan, etc. </p>
<p>Thank you for your input!</p>
<p><img src="https://i.stack.imgur.com/cQlpU.jpg" alt="Green color spectrum"></p>
| [
{
"answer_id": 3877,
"pm_score": 4,
"text": "<blockquote>\n <p>I've read somewhere that humans are most capable of distinguishing shades of green, that is a human can differentiate more shades of green than any other color. Is it true?</p>\n</blockquote>\n\n<p>I'd say it's <strong>plausible</strong>, d... | [
{
"answer_id": 3874,
"pm_score": 2,
"text": "<p>Light is either monochromatic, or a combination of different wavelength in different proportions.</p>\n\n<p>In the eye, there're 4 types of sensor cells: one is greyscale-only, another 3 is for color vision. See <a href=\"http://en.wikipedia.org/wiki/Spect... |
3,888 | <p>I recall a story from one of my Botany professors where he encountered a woman picking <em>Solanum dulcamara</em> (nightshade) berries. When he asked her what she was doing with them, she responded that her husband had her make a pie from them every year. </p>
<p>As her husband was presumably still alive, and since I regard this particular professor as reliable, what would have removed enough solanine from the berries to avoid ill effects? Does the concentration decrease upon ripening, or would cooking destroy the toxin? Would that also be why we fry green tomatoes?</p>
<p>(As a disclaimer, no-one should eat plants that are known to be poisonous. Even though some people don't react to poison ivy, it is still a bad idea to rub it all over your body.)</p>
| [
{
"answer_id": 3896,
"pm_score": 3,
"text": "<p>If you ask Dr. Duke's phytochemical database, by far the most solanine is found in green potatoe <strong>fruits (their skin)</strong>, with much less in leaves and tissues. Similar values are seen in green tomatoes, with dozens of mg per 100g fruit. There ... | [
{
"answer_id": 23260,
"pm_score": 1,
"text": "<p>First of all there is no solanine in green tomato, there wasn't, and there never will be.</p>\n\n<blockquote>\n <p>Steroidal glycoalkaloids (SGAs) extracted from tomato leaves and\n berries (Lycopersicon esculentum Mill.) were separated and identified\n... |
3,905 | <p>Do plants grow differently when given sun light, wolfram lamp, fluorescent light, LED light, infrared, ultraviolet, x-ray, unfocused laser and stroboscope?</p>
| [
{
"answer_id": 3908,
"pm_score": 4,
"text": "<p>It matters a lot.\nTake a look at this graph:\n<img src=\"https://i.stack.imgur.com/VYS0X.png\" alt=\"enter image description here\"></p>\n\n<p>This graph is for the \"normal\" plants containing <a href=\"http://en.wikipedia.org/wiki/Chlorophyll\" rel=\"no... | [
{
"answer_id": 36608,
"pm_score": 1,
"text": "<p>Color of light matters. As the Answer with the graph shows, chlorophyll absorbs certain colors of light best. It is strange that it does not seem to absorb yellow light well, considering that the sun has the highest emission level there, but perhaps it wa... |
3,918 | <p>I was reading a <em>Scientific American</em> story, “Controversial Spewed Iron Experiment Succeeds as Carbon Sink” (by David Biello), when I came across this sentence:</p>
<blockquote>
<p>“The problem for scientists is that oceanic waters tend to mix, which
makes monitoring and <em>delineating an experiment</em> in the ocean
challenging.”</p>
</blockquote>
<p>I'm wondering what “<strong>delineate</strong>” means in this context. I think I grasp the general idea of this sentence, but it is the exact meaning of the word that has been troubling me.</p>
<p>Could someone kindly enlighten me on this?</p>
<p>Thanks!</p>
| [
{
"answer_id": 3908,
"pm_score": 4,
"text": "<p>It matters a lot.\nTake a look at this graph:\n<img src=\"https://i.stack.imgur.com/VYS0X.png\" alt=\"enter image description here\"></p>\n\n<p>This graph is for the \"normal\" plants containing <a href=\"http://en.wikipedia.org/wiki/Chlorophyll\" rel=\"no... | [
{
"answer_id": 36608,
"pm_score": 1,
"text": "<p>Color of light matters. As the Answer with the graph shows, chlorophyll absorbs certain colors of light best. It is strange that it does not seem to absorb yellow light well, considering that the sun has the highest emission level there, but perhaps it wa... |
3,920 | <p>I came across a confusing word when I was reading a <em>Scientific American</em> <a href="http://www.scientificamerican.com/article.cfm?id=fertilizing-ocean-with-iron-sequesters-co2" rel="nofollow">story</a>, “Controversial Spewed Iron Experiment Succeeds as Carbon Sink” (by David Biello). It goes like this:</p>
<blockquote>
<p>“One key to the whole experiment’s success turns out to be the
specific diatoms involved, which use silicon to make their shells and
tend to form long strands of cellular slime after their demise that
falls quickly to the seafloor.”</p>
</blockquote>
<p>I'm wondering what “<strong>cellular</strong>” means in this context. Does it mean “<strong>of (diatom) cells</strong>” or “<strong>porous</strong>”?</p>
<p>Could someone kindly enlighten me on this?</p>
| [
{
"answer_id": 3921,
"pm_score": 2,
"text": "<p>My understanding is that the slime in question is formed of the bodies (the cells) of the dead diatoms. Where does porous come into it? Is it mentioned in a previous sentence?</p>\n"
}
] | [
{
"answer_id": 39947,
"pm_score": 0,
"text": "<p>'Cellular' in this context simply refers to slime of (diatom) cellular origin. The word 'cellular' is not referring to porosity. It appears the author wanted to be clear that the slime is from the cell, and not of some other origin. Perhaps the distinctio... |
4,924 | <p>I'm having problems with data analysis here.</p>
<p>I have flow cytometry data being collected on a Fortessa, and when I import them into FlowJo 8.7, all of my fluorescence values are systematically 10X lower than they are on the cytometer. No idea what's going on here, anybody can help? If you want screenshots and photos of the data, I'm happy to post them up.</p>
| [
{
"answer_id": 3921,
"pm_score": 2,
"text": "<p>My understanding is that the slime in question is formed of the bodies (the cells) of the dead diatoms. Where does porous come into it? Is it mentioned in a previous sentence?</p>\n"
}
] | [
{
"answer_id": 39947,
"pm_score": 0,
"text": "<p>'Cellular' in this context simply refers to slime of (diatom) cellular origin. The word 'cellular' is not referring to porosity. It appears the author wanted to be clear that the slime is from the cell, and not of some other origin. Perhaps the distinctio... |
4,935 | <p>I have just read <a href="https://biology.stackexchange.com/questions/3652/what-elements-are-a-possible-basis-for-life">What elements are a possible basis for life?</a> and I find myself wondering whether instead of seeking advanced life-forms at remote locales a La SETI, and perhaps fundamentally differently, we ought to be looking for similar microscopic life forms on comets that pass off-and-on.</p>
<p>Granted, a comet may be near absolute 0 for a lot of the time, but microscopic life-forms are known to be capable of surviving lean periods by using a cyst, for instance. As far as the rest is concerned, comets probably contain some amount of ice, and hence water, too. Similarly a comet's sprint around the sun could provide some limited amount of gravity/mass too.</p>
<p>So, should we be looking for life on comets?</p>
| [
{
"answer_id": 4939,
"pm_score": 3,
"text": "<p>Yes we should be and we are! Scientists have been analysing cometary material - but its a challenging task. The problem with looking at meteoritic material from comets on Earth is that it is generally contaminated with material <em>from</em> Earth. In addi... | [
{
"answer_id": 4937,
"pm_score": 2,
"text": "<p>This is a cool idea and definitely we have found a lot of the chemicals important to life are associated with comets which have a lot of water too. </p>\n\n<p>Another issue besides the v. low temperatures on comets, when they warm up to the sun are not lon... |
4,995 | <p>I am currently reading "<a href="http://www.amazon.co.uk/Chemistry-Life-Penguin-Press-Science/dp/0140272739/ref=sr_1_1?ie=UTF8&qid=1350994643&sr=8-1" rel="noreferrer">The Chemistry of Life</a>" by Rose. It's a great book (to me as a lay reader at least) and an interesting topic so I am interested in pursuing some of the further reading he suggests. </p>
<p>The first book he mentions in the bibliography is Alberts' "<a href="http://www.amazon.co.uk/Molecular-Biology-Cell-Bruce-Alberts/dp/0815341067/ref=sr_1_1?s=books&ie=UTF8&qid=1350994879&sr=1-1" rel="noreferrer">Molecular Biology of the Cell</a>". Looking at the description and the reviews it seems that this is a pretty advanced bio-sciences graduate level text, and I am very much not that. I see that Alberts has also written "<a href="http://www.amazon.co.uk/Essential-Cell-Biology-Bruce-Alberts/dp/081534130X/ref=sr_1_2?s=books&ie=UTF8&qid=1350995133&sr=1-2" rel="noreferrer">Essential Cell Biology</a>" which looks more accessible. Before I buy this I wondered if anyone can explain the difference, which would be a better read for an enthusiastic amateur?</p>
<p>If it helps at all I am a science grad and I typically read authors such as Dawkins and Matt Ridley, but I'm looking for something a little bit more rigorous to expand my knowledge in cell biology.</p>
| [
{
"answer_id": 4996,
"pm_score": 4,
"text": "<p>Might as well make it into an answer. As I said in the comments, Albert's \"Molecular Biology of the Cell\" is the classic textbook for Biology undergraduates. It has been so for decades now. </p>\n\n<p>It starts from the basics and builds up. Anyone with... | [
{
"answer_id": 4997,
"pm_score": 3,
"text": "<p>I've actually got a copy of Essential Cell Biology on my desk currently, it's one of our core textbooks. </p>\n\n<p>When comparing with the \"look inside\" feature on Amazon for Molecular Biology of the Cell (remembering I only have access to the first fe... |
5,010 | <p>I'm a mathematician trying to test some things on gene expression data, and I'm thus skimming over various articles such as <a href="http://www.ncbi.nlm.nih.gov/pubmed?term=Sotiriou%20et.%20al.%2C%20Breast%20cancer%20classification%20and%20prognosis%20based%20on%20gene%20%20expression%20profiles%20from%20a%20population-based%20study." rel="nofollow">Sotiriou et. al.</a> to understand what is typically done with such data sets. Several things confuse me; in particular, a paragraph in <a href="http://www.ncbi.nlm.nih.gov/pubmed?term=Sotiriou%20et.%20al.%2C%20Breast%20cancer%20classification%20and%20prognosis%20based%20on%20gene%20%20expression%20profiles%20from%20a%20population-based%20study." rel="nofollow">Sotiriou et. al.</a> reads:</p>
<p><em>"Clinical parameters such as ER status, [...] affect the behavior of breast
cancers. We asked whether these clinical/pathologic characteristics were
associated with differential gene expression. Parametric t tests identified 606
probe elements of 7,650 elements represented in our array that could segregate
ER+ and ER- breast tumors (P < 0.001)."</em></p>
<p>As segregation of ER+/- based on gene expressions is one of several things I'm
interested in attempting to achieve through novel methods, I have been trying
to understand what precisely is meant with the above paragrah. To recap the
article, there are 99 patients with 7,650 probe expression values, and one
ER+/- value each. The article sets out to determine which of those 7,650
probes successfully segregate the dataset into ER+ and ER-.</p>
<p>I've run the above paragraph by a nearby statistician, and he could not for
the life of him figure out what was done, and had not even heard of such a
thing as a "parametric t test". This leads me to suspect that the term is
specific to biology, so I ask: what is meant? It is also unclear to me (and
him) what the P-value means in this context.</p>
<p>I hope the scope of this question isn't too broad. Of course I want to avoid
asking "explain this article to me, the outsider, please"; I do believe the
paragraph above is relatively self-contained in the context of gene
expression.</p>
<p>References:</p>
<ol>
<li><a href="http://www.ncbi.nlm.nih.gov/pubmed?term=Sotiriou%20et.%20al.%2C%20Breast%20cancer%20classification%20and%20prognosis%20based%20on%20gene%20%20expression%20profiles%20from%20a%20population-based%20study." rel="nofollow">Sotiriou et. al., Breast cancer classification and prognosis based on gene
expression profiles from a population-based study.</a></li>
</ol>
| [
{
"answer_id": 5012,
"pm_score": 4,
"text": "<p>I understand this in the following way:</p>\n\n<p>For each probe you have two sets of measurements, one for ER+ and one for ER-. What you do is a T-test (to my understanding is that the \"parametric\" just emphasizes that T-test is a parametric test) on th... | [
{
"answer_id": 5011,
"pm_score": 2,
"text": "<p>This isn't the answer you're probably looking for, but I'd recommend not bothering with what they mean about their test in particular ... maybe they were really using a mann-whitney but their software (SPLUS) labeled it as a \"non-parametric t test\" for t... |
5,043 | <p>I'm wondering what produces the feeling of hunger in humans. Checking Wikipedia revealed that leptin and ghrelin are two hormones involved. I've also read that the digestive system produces its own melatonin.</p>
<p>Because melatonin is related to circadian rhythm and the biological clock,<em>Is melatonin involved in feeling hungry?</em> <strong>Is there a circadian pattern to the levels of leptin and ghrelin in humans?</strong> </p>
| [
{
"answer_id": 5071,
"pm_score": 3,
"text": "<p><strong>Yes</strong>, absolutely. A major focus of understanding obesity, diabetes and other metabolic disorders are targeted to understanding the circadian (and other cyclical nature) systems in neurobiology and endocrinology. I can speak within the study... | [
{
"answer_id": 5084,
"pm_score": 0,
"text": "<p>I found additional information on the subject. Apparently Serotonin is also involved in feeling hunger and the motivation to eat. It also follows a diurnal/circadian pattern as described below:</p>\n\n<p><a href=\"http://en.wikipedia.org/wiki/Serotonin#Gau... |
5,056 | <p>I was just reading <a href="http://www.slate.com/articles/health_and_science/human_evolution/2012/10/evolution_of_lactose_tolerance_why_do_humans_keep_drinking_milk.single.html">Evolution of lactose tolerance</a>, and in it one line says "But there was a time in human history when our diet and environment conspired to create conditions that mimicked those of a disease epidemic". </p>
<p>Something I've always wondered is rather than natural selection occurring and survival of the fittest and so on, is that a viral epidemic caused a mutation in the survivors, i.e. DNA was inserted from the virus that modified the survivors genome. There is some evidence that a significant percentage of the human genome comes from viruses. Probably a naive question - so is there any evidence that this has occurred? From my lay perspective this is what attempts at genetic engineering use, so it's possible nature already did this?</p>
<p>It's always seemed to me that natural selection and point mutations, and the chance meeting of two people with the same mutation would be too slow and viruses would be a more efficient method to evolve a large population at the same time. Things like punctuated evolution might support this? not really sure.</p>
| [
{
"answer_id": 5071,
"pm_score": 3,
"text": "<p><strong>Yes</strong>, absolutely. A major focus of understanding obesity, diabetes and other metabolic disorders are targeted to understanding the circadian (and other cyclical nature) systems in neurobiology and endocrinology. I can speak within the study... | [
{
"answer_id": 5084,
"pm_score": 0,
"text": "<p>I found additional information on the subject. Apparently Serotonin is also involved in feeling hunger and the motivation to eat. It also follows a diurnal/circadian pattern as described below:</p>\n\n<p><a href=\"http://en.wikipedia.org/wiki/Serotonin#Gau... |
5,059 | <p>In protocols for minimal media for growing bacteria I often see that a vitamin mix or a mix of various trace metals is added. But at least for E. coli I know that those are not strictly necessary, they also grow in minimal medium without any of this.</p>
<p>Does it make sense to add vitamins or trace elements when growing common E. coli for protein expression like BL21 (DE3) in minimal medium? Is there some literature data on how this can affect the growth of the bacteria?</p>
| [
{
"answer_id": 5061,
"pm_score": 3,
"text": "<p>Not sure that I have ever come across trace metals in recipes (I assume that you aren't referring to the Ca/Mg salts component of M9), but it is certainly the case that many K12 strains (e.g. C600, DH5α) require thiamine because they are <em>thi</em>... | [
{
"answer_id": 73816,
"pm_score": 0,
"text": "<p>Adding trace elements (Fe, Co) and vitamins will increase the growth rate of E coli quite significantly. </p>\n\n<p>However in the context of protein expression, more is sometimes not better. The proteins produced under high yield conditions may be miss-f... |
5,074 | <p>The theory of natural selection has it that individuals with better genes tend to survive and reproduce, passing their genes to their offspring. This gradual process results in a population more adapted at survival. However, due to the advancement in medical science, humans with poorer genes tend to survive and reproduce just as well.</p>
<p>For example, in the past, many people, excluding those with natural immunity due to some genetic mutations, would have succumbed to illnesses such as malaria and typhoid. But with better hygiene and medical treatment, these patients tend to survive.</p>
<p>Now, imagine a future where all illnesses including cancer can be treated. How would it impact the survival of the human race? Would we become more and more vulnerable such that our survival hinges heavily on medical technology, analogous to how an astronaut's survival is dependent on his spacesuit?</p>
| [
{
"answer_id": 5080,
"pm_score": 4,
"text": "<p>Gene frequencies (frequencies of each allele at a given loci) in populations are affected by many things divided in to systematic and dispersive processes. Systematic process (migration, mutation, selection) affect gene frequencies in an often quite predic... | [
{
"answer_id": 5075,
"pm_score": 3,
"text": "<blockquote>\n <p>The theory of natural selection has it that individuals with better genes tend to survive and reproduce, passing their genes to their offspring.</p>\n</blockquote>\n\n<p>Yes, under <strong>selective pressure</strong>, that is. The stronger ... |
5,077 | <p>I'm trying to construct an anaerobic kitchen-waste digester at home.</p>
<p>The major output from the digester is methane - with a significant component of carbon dioxide. To scrub/reduce the CO2 I was thinking of passing the methane through a freshwater container charged with algae ... then it occurred to me to also think of introducing some bioluminescent algae to drive the photosynthesis & absorb some of the oxygen released by the other algae. Understandably this would be an unbalanced system.</p>
<p>But ... can bioluminescence drive photosynthesis?</p>
| [
{
"answer_id": 5083,
"pm_score": 4,
"text": "<p>Yes and no. Yes as in the energetics do work out and you will be going down a small but non-trivial driving force as long as you continue to provide the luciferin to the algae.</p>\n\n<p>However, the wavelengths of light by which photosynthesis absorbs its... | [
{
"answer_id": 88757,
"pm_score": 1,
"text": "<p>Curiously enough, this was the subject of a paper in 2013. The authors claimed to have driven photosynthesis by submerging some dark-adapted leaves into a solution containing a mixture of luminol, hydrogen peroxide and horseradish peroxidase (HRP).</p>\n\... |
5,090 | <p>I'm wandering if mammals that can eat many different kinds of food <strong>(omnivores) vary their preference for food not only based on the availability, but also based on dietary needs?</strong> </p>
<p>I'm looking at this site <a href="http://nutritiondata.self.com/">Food nutritional content</a> and see that "not all foods are created equal" - the vitamin/mineral and amino acid contents can vary dramatically. <strong>Is there some part of an omnivore brain/digestive system that "monitors" the micronutrient density of digested food and adjusts food preferences</strong> towards foods that make the diet more complete?</p>
| [
{
"answer_id": 5106,
"pm_score": 3,
"text": "<p>For what concerns amino acids, mice rapidly reject meals that are not balanced in essential amino acids and continue to look for other kind of foods. This behavior is called <strong>aversion response</strong> and it is an adaptive phenomena that can be obs... | [
{
"answer_id": 5094,
"pm_score": 0,
"text": "<p>I found that there are seasonal rhythms in the nutrient intake:\n<a href=\"http://www.sciencedirect.com/science/article/pii/003193849190527U\" rel=\"nofollow\">Seasonal rhythms of human nutrient intake and meal pattern</a></p>\n\n<p>The article's abstract ... |
5,097 | <p>I'm reading about various parts of the human body and brain and started to wander if there's a branch of biology that deals with the entire human? I know that there are branches various -biologies, from neurobiology to something like heliobiology or chronobiology. All of them look at different organ systems or parts of an organism, but from different points of view.</p>
<p>Then there are sciences that deal with behavior and cognition of humans.</p>
<p>As I read about these, I notice that there's quite a lot of overlap, particularly when neurotransmitters and hormones are involved. For example Melatonin, a hormone has functions in both the brain and the gut. </p>
<p><strong>I'm wandering if there's some form of biology or science that deals with the entire organism, its behavior , as well as its parts?</strong> Am I thinking about Biology or Medicine or something else?</p>
| [
{
"answer_id": 5101,
"pm_score": 3,
"text": "<p>I was thinking of <a href=\"http://en.wikipedia.org/wiki/System_biology\" rel=\"nofollow\"><em>Systems/Integrative/Predictive Biology</em></a> reading your question. Studying the wikipedia entry it looks like a research approach with many problems trying t... | [
{
"answer_id": 5100,
"pm_score": 1,
"text": "<p>Medicine applies to healing illnesses of the body (with many subspecialties, including endocrinology which you may be interested in). Physiology is a branch of science which deals with the normal function of the body and its various parts. </p>\n"
}
] |
5,107 | <p>I have heard Sydney Brenner give a talk [0] on how the entire program of Systems Biology is suspect because, according to him, a chap named Hadamard showed that inverse problems are impossible to solve, or something to that effect. </p>
<p>I find it somewhat odd that no one seems to be paying any attention to this, and many are blithely carrying along trying to reverse-engineer biological organisms. I personally think that this reverse-engineering effort has its place, but Sydney Brenner doesn't seem to think so, and advocates tackling only the forward problem. Here's an excerpt from an abstract to a similar talk of his: </p>
<blockquote>
<p>... This notion of computation is, in my opinion, the only valid approach to biological complexity and is opposed to many of the ideas underlying what has come to be called systems biology, which is very fashionable today. It will be shown that systems biology attempts to solve inverse problems — that is, obtain models of biological systems from observations of their behaviour — whereas, what I call computational biology, continues in the classical mode of discovering the machinery of the system and computing behaviour, solving a forward problem.</p>
</blockquote>
<p>Is Brenner simply wrong on this or is there something to his objections?</p>
<hr>
<p>[0] Sydney Brenner, <a href="http://thesciencenetwork.org/programs/reading-the-human-genome-with-sydney-brenner/much-ado-about-nothing-systems-biology-and-inverse-problems" rel="nofollow noreferrer">Much ado about nothing: systems biology and inverse problems</a>, 2009.</p>
| [
{
"answer_id": 5110,
"pm_score": 5,
"text": "<p>The answer is mostly no, and this is not as disruptive a statement as it seems to be. </p>\n\n<p>I think Brenner has a point of course and he is not the only one who wonders whether the systems biology can create a holistic model of living things. Still I... | [
{
"answer_id": 5174,
"pm_score": 3,
"text": "<p>The article is well known and discussed amongst systems biologists. It makes a good point - high throughput, observational biology cannot substitute for mechanistic studies that provide causal information.</p>\n\n<p>But we know an awful lot about biologica... |
5,108 | <p>I am reading about the effect of extracellular potassium and chloride on the membrane potential, and now a question has come to my mind about what would happen if we added some molecules that have no charge to the extracellular? (consider that only K+ and Cl− can cross the membrane.)</p>
<p>I think that membrane potential and volume does not change, but I'm not sure about that.</p>
| [
{
"answer_id": 5111,
"pm_score": 3,
"text": "<p>The absolute answer would depend on a lot of factors, but the basics of it would be that - <strong>Yes</strong>, the volume does change and <strong>Yes</strong>, it would have an affect on the membrane potential.</p>\n\n<p>By adding mass to any liquid solu... | [
{
"answer_id": 5112,
"pm_score": 1,
"text": "<p>I'm no electrophysiologist, but I do know that the membrane potential is determined by the distribution of ions across the membrane: mostly Na<sup>+</sup>, K<sup>+</sup>, Ca<sup>2+</sup> and Cl<sup>-</sup>.</p>\n\n<p>An uncharged molecule will only influen... |
5,115 | <p>I'm reading an essay on the creating of the <em>Mammalia</em> zoological classification (Londa Schiebinger, <em>The American Historical Review</em>, Vol. 98, No. 2 (Apr., 1993), pp. 382-411).</p>
<p>It contains the statement (page 386)</p>
<blockquote>
<p>All mammals (including the whale) have hair, and it is still today considered a distinguishing characteristic of mammals. </p>
</blockquote>
<p>Is that statement correct? Do all known species of whale and dolphin have hair? If so, where is it? You can't see it on the surface of the animal, is it internal like we have nostril hair?</p>
| [
{
"answer_id": 5120,
"pm_score": 4,
"text": "<p>Well, technically yes, but <a href=\"http://en.wikipedia.org/wiki/Dolphin\">most adult dolphins do not have hair</a>:</p>\n\n<blockquote>\n <p>Unlike most mammals, dolphins do not have hair, <strong>except for a few hairs around the tip of their rostrum (... | [
{
"answer_id": 105615,
"pm_score": 2,
"text": "<p>I'll echo what others have said here. It is a characteristic of marine mammals as mammals. But not something you'd obviously see on adult whales. Humpback whales do have visible hair follicles. Another example where you can see hairs well are on gray wha... |
5,123 | <p>Yesterday my grandmother ate fresh tuna at a friend's party. She swears it was fresh and bought at a local fishmonger. The problem is, that we live in <a href="https://maps.google.com/maps?q=Gda%C5%84sk,%20Polska&hl=pl&ie=UTF8&ll=56.559482,17.138672&spn=14.159361,40.561523&sll=54.361087,18.690027&sspn=0.233253,0.633774&oq=Gda%C5%84sk,&t=h&hnear=Gda%C5%84sk,%20pomorskie,%20Polska&z=5" rel="nofollow noreferrer">Gdańsk</a>, by the south-eastern side of the Baltic sea and I have never heard of tuna in the Baltic. I told her that the fish couldn't have been local and therefore couldn't have been fresh but frozen and thawed. But the thought still bothers me, maybe tuna fish can reach the Baltic?</p>
<p>I did search a bit and found that tuna may be sometimes found in the Northern sea, so maybe it actually can travel so far east as to reach the Baltic? But the water in the Baltic is hardly saltwater (6-8‰), so would it be able to survive?</p>
| [
{
"answer_id": 5120,
"pm_score": 4,
"text": "<p>Well, technically yes, but <a href=\"http://en.wikipedia.org/wiki/Dolphin\">most adult dolphins do not have hair</a>:</p>\n\n<blockquote>\n <p>Unlike most mammals, dolphins do not have hair, <strong>except for a few hairs around the tip of their rostrum (... | [
{
"answer_id": 105615,
"pm_score": 2,
"text": "<p>I'll echo what others have said here. It is a characteristic of marine mammals as mammals. But not something you'd obviously see on adult whales. Humpback whales do have visible hair follicles. Another example where you can see hairs well are on gray wha... |
5,128 | <p>Our eyes are spherical, our retina is circular, but still our eyes can see more in the horizontal direction than in vertical direction. Why is it so, why is the preferred aspect ratio not square? </p>
| [
{
"answer_id": 5136,
"pm_score": 4,
"text": "<p>I found the explanation given below <a href=\"http://boards.straightdope.com/sdmb/showthread.php?t=300997\" rel=\"noreferrer\">here</a> (my emphasis). It may not be authoritative, but it makes sense to me.</p>\n<blockquote>\n<p>You can determine the approx... | [
{
"answer_id": 11188,
"pm_score": 2,
"text": "<p>The reasons your field of view is not circular are:</p>\n\n<ul>\n<li><p>Even when looking directly forward your nose, brows, and cheeks obstruct your view.</p></li>\n<li><p>You have two eyes which are aligned horizontally.</p></li>\n</ul>\n\n<p>The field ... |
5,137 | <p>What is the physical mechanism that causes temperature to rise during a fever? I know that somehow the hypothalamus "orders" to increase the standard body temperature regulation, and this should stimulate mitochondria to produce more ATP. Is that right? </p>
<p>Is this the only heating physical mechanism (through increasing production of ATP) that acts during a fever?</p>
| [
{
"answer_id": 8742,
"pm_score": 4,
"text": "<p>As John mentioned, pyrokines such as IL1 and TNF affect the hypothalamus. Your hypothalamus is a thermostat, similar to central heating for example. So when you set your core temperature higher, your body thinks it is cold. To warm up it does several thing... | [
{
"answer_id": 8739,
"pm_score": 1,
"text": "<p>Cytokine production in the body resets the thermoregulatory centre in the hypothalamus to a higher temperature. As a result, your muscles begin to contract violently (rigors) to generate more heat until you equilibrate to the new setpoint. Hope this helps.... |
5,152 | <p>Why exactly is HDL-cholesterol good for us and LDL-cholesterol bad for us. It has been well-established that LDL-cholesterol is associated with atherosclerosis and that HDL-cholesterol helps remove excess LDL-cholesterol from the circulation. From a biochemical view, however, what is the difference between the molecules that causes this difference?</p>
| [
{
"answer_id": 5154,
"pm_score": 5,
"text": "<p>First of all, we should specify that <strong>there is no such thing as \"HDL-cholesterols\" and \"LDL-cholesterols\"</strong>. On the same note <strong>there is no such thing as \"good cholesterol\" and \"bad cholesterol\"</strong>: cholesterol is just one... | [
{
"answer_id": 105112,
"pm_score": 0,
"text": "<p>Your question is about the molecular differences between LDL and HDL.</p>\n<p>The way you formulate, asking about differences on the molecular level, draws the attention to the surprising fact that the molecular structure is not that different as the b... |
5,156 | <p>While eating sour food or candy, I start to sweat if it's sour enough. My body feels much hotter although my actual temperature is the same, my forehead starts sweating a lot and I feel like it just got twice as hot wherever I am. </p>
<p>Is this a biological phenomena or is my DNA just stupid? Is it somehow related to the digestive system, that sour food is harder to digest?</p>
| [
{
"answer_id": 5161,
"pm_score": 3,
"text": "<p>In general, sweating is caused by too much heat, even if you're not aware of the heat. This can happen if the bowel moves and so raises the core temperature. Such movement is often accompanied with sweating, and since you only feel the normal temperature o... | [
{
"answer_id": 5159,
"pm_score": 1,
"text": "<p>I don't think this is a normal physiological response, but I would seek medical advice to be sure.</p>\n\n<p>I did a quick literature search with keywords \"sour\", \"food\" and \"sweating\" and came up with one article about <a href=\"http://www.ncbi.nlm.... |
5,162 | <p>ATP Synthase is ubiquitous throughout life on earth and so most probably evolved within the last universal common ancestor (LUCA) before that lineage diversified into the various kingdoms of life. </p>
<p>It is suggested that the functional domains comprising the ATP Synthase complex were cobbled together from pre-existing sub-units, each with with a related activity (e.g. the union of a proton motor with a DNA Helicase with ATPase activity), which seems reasonable, although a bit vague in the details. </p>
<p>The fact that a primitive ATP Synthase arose in the first place suggests that ATP already had a central role in cellular metabolism and so begs the question, what preceded ATP Synthase in the role of generating ATP in the LUCA cell? </p>
| [
{
"answer_id": 5169,
"pm_score": 4,
"text": "<p>There are metabolic processes in which ATP is synthesised without the involvement of ATP synthase. The best examples are, in fact, two steps in the <a href=\"http://en.wikipedia.org/wiki/Glycolysis\">glycolytic pathway</a>, catalysed by phosphoglycerate ki... | [
{
"answer_id": 80625,
"pm_score": 0,
"text": "<p>We don't know much about early evolution of life. However it is believed that energetic molecules (analogous to ATP) may have evolved before everything else. These energetic molecules may have driven different metabolic reactions (which need not be cataly... |
5,164 | <p>Why did Darwin formulate his theory of evolution just after his visit to the Galápagos islands? Why were they so special from an evolutionary point of view?</p>
| [
{
"answer_id": 5168,
"pm_score": 5,
"text": "<p>Charles Darwin formulated his theory after travelling the world aboard the Beagle, here's <a href=\"http://upload.wikimedia.org/wikipedia/commons/4/42/Voyage_of_the_Beagle.jpg\" rel=\"nofollow\">the route</a>. He found the Galapagos Islands particularly in... | [
{
"answer_id": 5167,
"pm_score": 3,
"text": "<p>Galápagos islands are one of few islands with a unique fauna and flora. This can only happen when the distance to other land is great enough, and when the island exists long enough that flora and fauna could grow (volcano islands are sterile for a long tim... |
5,171 | <p>A lot of people live in a 7 day cycle, where 5 days of work are followed by 2 days of "rest". Vacations and holidays can increase the time available for resting. </p>
<p><strong>Is there any biological reason for humans to rest after x days of work?</strong> Can this be explained by the buildup of by-products of metabolism, like <a href="http://en.wikipedia.org/wiki/Homocysteine">Homocysteine</a>?</p>
| [
{
"answer_id": 5176,
"pm_score": 3,
"text": "<p>I think your main assumption is not true -- we do not really rest on weekends.</p>\n\n<p>I do not know many people who only rest on weekends. Usually this is the time for socializing, doing home-related work, physical activity (sports, hiking), spending ti... | [
{
"answer_id": 16666,
"pm_score": 0,
"text": "<p>Our bodies work in cycles.. Circadian cycles that refer to our daily routines. We need sleep every night, eating at night affects us differently than if eating in the morning, etc... all because our bodies functions work in these 24 hour cycles... \nNow, ... |
5,191 | <p>What is the actual biological difference between mice and rats? Are they actually the same thing with two different names depending on appearance (are they all mice for instance and we call the larger ones rats or vice versa) or is there some fundamental difference in their genetics?</p>
| [
{
"answer_id": 5192,
"pm_score": 4,
"text": "<p>Mice (<em>Mus</em>) and rats (<em>Rattus</em>) are definitely separate species, by whichever <a href=\"http://research.amnh.org/vz/ornithology/crossbills/species.html\" rel=\"noreferrer\">definition of species</a> you choose to use. They are genetically di... | [
{
"answer_id": 5193,
"pm_score": 3,
"text": "<p>True rats and mice are rodents that constitute part of the subfamily <em>Murinae</em> in the family <em>Muridae</em>. The Old World house mouse is <em>Mus musculus</em>, the brown rat is <em>Rattus norvegicus</em>, so they are members of two different gene... |
5,194 | <p>I've heard that the brain consumes quite a lot of oxygen and energy, compared to the rest of the body. <strong>What I'm interested in is if this is the kind of energy and oxygen that the rest of the body competes for?</strong></p>
<ul>
<li>For example, does running divert resources from the brain to the
muscles, leading to decreased cognitive performance?</li>
<li>Does digesting food divert resources from the brain to the gut?</li>
</ul>
<p>Does the heart rate or blood pressure have anything to do with how much resources, like oxygen and energy are available to neurons?</p>
<p>Thank you for your input!</p>
| [
{
"answer_id": 5196,
"pm_score": 4,
"text": "<p>You can grab any university level text on human physiology and you will find that the brain is a unique organ for cellular respiration. The brain is only capable of using two metabolic subtrates: glucose for oxidative phosphorylation (producing ATP) and ke... | [
{
"answer_id": 5195,
"pm_score": 2,
"text": "<p>While in general the answer is \"yes\", the brain does use the same type of resources as other parts of the body, you cannot from that alone derive conclusions about the brain competing with other organs. Also, I think that cognitive performance is not a f... |
5,202 | <p>I've heard the following idea this morning: Before the introduction of contraception, humans conceived quite a lot of babies (there was little to do to avoid that), but the population was kept in check by very high childhood mortality rates. This mortality rate ensured that <strong>only the fittest survived.</strong></p>
<p>The idea seems common sense, but I decided to investigate if this is really true. I know that for evolution, even 2000 years should be an instant. </p>
<p>I did some research, for example the worst <a href="http://en.wikipedia.org/wiki/Infant_mortality#Global_trends" rel="nofollow noreferrer">childhood mortality</a> rate currently in the world is around 17.5%, which is still about half of what it was in "developed" countries during the 1700s, according to the table below. But looking at the wikipedia map of childhood mortality, it seems that a baby nowadays has only around 1-3% chance of dying before adulthood, because even the weakest baby can be kept on life support long enough for the danger to pass. </p>
<p><strong>What are the implications of reducing childhood mortality rates worldwide on human evolution?</strong> Maybe evolution is a wrong term to use here. Would it be fitness as species? I'm particularly interested in how this relates to developmental defects and genetic disorders. <strong>Is there any evidence that people who lived in a world without contraception and with high childhood mortality rate were more physically or mentally fit?</strong></p>
<p>Here's an paper that deals with the subject and the table is from the paper below:</p>
<p><a href="http://shell.newpaltz.edu/jsec/articles/volume2/issue4/NEEPSvolkatkinson.pdf" rel="nofollow noreferrer">IS CHILD DEATH THE CRUCIBLE OF HUMAN
EVOLUTION?</a></p>
<p><img src="https://i.stack.imgur.com/VtHB5.png" alt="Childhood Mortality Rates"></p>
| [
{
"answer_id": 5209,
"pm_score": 3,
"text": "<blockquote>\n <p>Before the introduction of contraception, humans conceived quite a lot of babies (there was little to do to avoid that), but the population was kept in check by very high childhood mortality rates. <strong>This mortality rate ensured that o... | [
{
"answer_id": 31014,
"pm_score": -1,
"text": "<p>Well , Ime sorry but sometimes a question have to be rephrased in order to reach the ''elefant in the room'' : The important question is if the existence of contraceptives in itself wil change the direction of human evolution . After the invention of c... |
5,234 | <p>I am fusing a protein with a Dam enzyme (<a href="http://en.wikipedia.org/wiki/Dam_%28methylase%29" rel="nofollow">http://en.wikipedia.org/wiki/Dam_(methylase)</a>). The idea is that when the protein binds to the DNA, the Dam enzyme will start methylating nearby GATC sites, thus helping identify the protein binding region (using DpnI later on, and microarray technology). However, I have no idea, in theory, how many (bps) will the enzyme traverse across the genome from its starting location. I.e., how far (in terms of bp) from its starting location will the enzyme methylate the GATC sites.</p>
<p>There are methods for finding protein binding regions along the genome that use such technology, such example here: <a href="http://www.nature.com/nbt/journal/v18/n4/abs/nbt0400_424.html" rel="nofollow">http://www.nature.com/nbt/journal/v18/n4/abs/nbt0400_424.html</a> </p>
| [
{
"answer_id": 5239,
"pm_score": 4,
"text": "<p><strong>Dam methyltransferase methylates large DNA molecules in a processive manner, with an effective range of up to 7 kb on either side of an initial methylation reaction.</strong></p>\n\n<p>My answer is taken from this paper:</p>\n\n<blockquote>\n <p>U... | [
{
"answer_id": 5236,
"pm_score": 2,
"text": "<p>After re-reading your question, I suspect you are conflating DNA methylation and restriction digestion. For a more detailed overview of how these two relate to each other, please read the <a href=\"http://www.neb.com/nebecomm/tech_reference/restriction_enz... |
5,249 | <p>In the normal function of the kidney, the bloodstream is near emptied of fluids as it moves through the glomerulus, in which glomerular filtrate is formed.</p>
<p>As it proceeds through the Nephron, a significant amount of this material is returned to the bloodstream, and only a comparatively timy amount goes into the urine. </p>
<p>Why, in evoultionary terms, is it not more favourable energetically to remove only the small number of molecules, perhaph using specialised channels made of protein and activated only by a certain molecules which need removing, at a potentially huge energy saving?</p>
| [
{
"answer_id": 5250,
"pm_score": 4,
"text": "<p>Probably because it's easier to retain what the body <em>wants</em> than get rid of what the body <em>doesn't want</em>. </p>\n\n<p>What does your body want to <strong>keep</strong> from your Urine? Pretty much water and selective ions (Cl-, K+, Na+, Ca+2,... | [
{
"answer_id": 5254,
"pm_score": 2,
"text": "<p>I would argue from an evolutionary perspective: not all kidneys are created equal. The mammalian kidney has a long evolutionary history and potentially a lot of phylogenetic inertia. Mammals do what they can with what they inherited from their ancestors.</... |
5,263 | <p>Botulinum toxin (trade name Botox) inhibits acetylcholine release in neurons and causes botulism, an acute paralytic disease which leads to nerve degeneration and takes a long time to recover. I've read the statement that Botox is the most potent poison we know a few times now and was wondering <em>why exactly</em> it is. All sources I've found only claim <em>that</em> it is, without explanation.</p>
| [
{
"answer_id": 5266,
"pm_score": 2,
"text": "<p>A quick search for a <a href=\"http://en.wikipedia.org/wiki/Median_lethal_dose\" rel=\"nofollow\">list of LD50</a> (median lethal dose; half of the people will die with that dosage) gave me 1 ng/kg for Botulinum toxin. This is pretty darn small amount, and... | [
{
"answer_id": 5282,
"pm_score": 2,
"text": "<p>The <a href=\"http://en.wikipedia.org/wiki/Botulinum_toxin#Biochemical_mechanism_of_toxicity\" rel=\"nofollow\">biochemical mechanism</a> of BT is pretty well laid out at Wikipedia already. The toxin is likely very potent because (1) it is targeted to neur... |
5,268 | <p>Why do living organisms spontaneously replicate itself or "procreate" (my understanding is that it does).</p>
<p>From a uni-cellular and micro-organism point of view. Is there some sort of stimulant in the environment? A chemical reaction that causes it? Is is there a physical or emotional motivation? Is it by choice?</p>
<p>Note: I may have some terms used wrongly as I am not a biologist. In this question, I am interested at living organism nearer the forms of single smallest unit of life form.</p>
| [
{
"answer_id": 5272,
"pm_score": 3,
"text": "<p>If there are enough nutrients, a unicellular organism will \"eat\" and grow until it reaches a certain size. Through different mechanisms, it can sense that it is large enough and has enough metabolites to divide. Then, the organism will duplicates its DNA... | [
{
"answer_id": 5270,
"pm_score": 2,
"text": "<p>This is a very interesting question but the answer (or as much of the answer as is known) can fill a few books. There are many many signals that control cell division. </p>\n\n<p>As a horrible simplification, the cell can be compared to a car parked on a s... |
5,273 | <p>I'm testing out various phylogenetic libraries in Python. I want to read in a Newick tree, then, given a list of taxa, generate the smallest tree that contains them all. This task is quite simple and efficient in dendropy and ete2:</p>
<pre><code>newick = '((raccoon, bear),((sea_lion,seal),((monkey,cat), weasel)),dog);'
taxa = ['raccoon', 'sea_lion']
import ete2
tree = ete2.Tree(newick)
pruned = tree.prune(taxa)
import dendropy
tree = dendropy.Tree.get_from_string(newick, 'newick')
pruned = tree.prune_taxa_with_labels(taxa)
</code></pre>
<p>I'm trying but failing to find equivalent functionality in the Bio.Phylo package. Trees do have a "prune" method, but it prunes a single node from the tree.</p>
| [
{
"answer_id": 5275,
"pm_score": 3,
"text": "<p>The <a href=\"http://biopython.org/DIST/docs/api/Bio.Phylo.BaseTree.TreeMixin-class.html#common_ancestor\" rel=\"nofollow\"><code>common_ancestor</code></a> function should give you the result you want: it gives you the tree (I think) that is the most rece... | [
{
"answer_id": 10785,
"pm_score": 1,
"text": "<p>Sorry for digging out this old question. But I think that given you have an unrooted tree, the common ancestor maybe not the correct answer.</p>\n\n<p>What you need to do is this:\nSuppose you have an unrooted tree with n tips (species), and thus 2n-3 bra... |
5,289 | <p>That is to say, are there cells that, between infancy and adulthood, get larger? Or is all growth done entirely via cell division? I'm wondering if it is safe to assume that the approximate number of cells per unit mass in a mammal will remain fairly constant throughout its lifespan. </p>
| [
{
"answer_id": 5290,
"pm_score": 3,
"text": "<blockquote>\n <p>I'm wondering if it is safe to assume that the approximate number of cells per unit mass in a mammal will remain fairly constant throughout its lifespan.</p>\n</blockquote>\n\n<p><em>Not exactly.</em> When a tissue is put under stress, it ... | [
{
"answer_id": 5292,
"pm_score": 2,
"text": "<p>This is not my field so I am sure there are other examples, but certain neurons will definitely be larger in adulthood than in infancy. There are motor neurons that connect the spine to, for example, the toes. These will grow in length as an animal grows. ... |
5,300 | <p>I'm aware of measures like number of distinct cell types being used as a measurement of complexity in biology, for example in the G-value paradox. But this doesn't really help for unicellular organisms. Is it possible to define a unit of complexity to make comparisons between different organisms?</p>
| [
{
"answer_id": 5351,
"pm_score": 3,
"text": "<p>This is a very interesting question. Not sure if there is any way to answer without specifying a definition for complexity.</p>\n\n<p>It is clear that everything is made of only the same few elements, so complexity must involve more than that. Do the numbe... | [
{
"answer_id": 5301,
"pm_score": 0,
"text": "<p>I don't know if it is helpful for your problem, but I measured complexity in gen regulatory networks by parsing them into boolean networks. Then you can initiate all nodes with a random boolean value and update the network until it reaches an attractor. Fo... |
5,304 | <p>Every time I get ill (cold, flu etc) I take a couple of these wonderful tablets for up to 4 times a day and I, eventually, get better. What exactly is paracetamol? Why is it so effective and is it really not harmful as my doctor would have me believe?</p>
| [
{
"answer_id": 5305,
"pm_score": 5,
"text": "<p>Paracetamol is a pain killer, it does not treat the cause of your illness, it only alleviates the symptoms. From its <a href=\"http://en.wikipedia.org/wiki/Paracetamol\" rel=\"noreferrer\">wikipedia page</a>:</p>\n<blockquote>\n<p>Paracetamol [...], chemic... | [
{
"answer_id": 5432,
"pm_score": 1,
"text": "<p>Paracetamol, also known as acetominophen and Tylenol is a Non Steroidal Anti Inflammatory Drug (NSAID). Other NSAIDs include aspirin and ibuprofen (Advil). </p>\n\n<p>NSAIDs all help with inflammation, reduce fever, but each has its own effect. Aspirin t... |
5,306 | <p>I've been reading about brain plasticity and how the brain can "rewire" itself. </p>
<p>One of the things that is not clear to me - how neurons can establish new connections. <strong>Does this rewiring mean that neurons can "disconnect" from other neurons to reuse existing dendrites</strong>? Or do neurons grow new dendrites to make these new connections, adding to existing ones? </p>
<p>Thank you for your input!</p>
| [
{
"answer_id": 5308,
"pm_score": 4,
"text": "<p>I haven't read anything particularly about dendrites being reshaped, though I would expect them to be as flexible as other parts of the cells.</p>\n\n<p>The more commonly discussed topic (in my literary experience) is reshaping of the axon's branches befor... | [
{
"answer_id": 65866,
"pm_score": 1,
"text": "<p>Under conditions where the sensory input to the cortex has been altered, large-scale changes in dendritic branching have been observed after enriched environment experience (e.g. Greenough and Volkmar, 1973) and sensory deprivation (e.g. Tailby et al. 200... |
5,403 | <p>As written in my lecture handouts, there two main factors in the Geometric Growth Model of populations:</p>
<p>$R_{0}$ is the expected lifetime reproductive output. This way, for unicellulars, for example, when time between division represents life time, if there is no mortality, $R_{0}$ is calculated as $R_{0}=1*2$, where 1 is 100% and 2 is the amount of daughter cells expected to be produced as a result of the mother cell split. We also define that for this isolated incident, $B$, the amount of births is 2, while the mother cell "dies", which leads to $D=1$.</p>
<p>The second factor is $\lambda$, which is the finite rate of increase, which in other words means that this is average per-capita multiplication factor per one time-step.
When we measure population growth in time-steps of 1 lifetime, we can conclude that $\lambda=R_0$. We actually look at $\lambda$ as at $\frac{N_{t+1}}{N_{t}}$, where $N_{t+1}=N_{t}+B-D$(1) and $N_t$ is the amount of individuals in the populations at time-step $t$. This way we define $\lambda$ using $b=\frac{B}{N_{t}}$ and $d=\frac{D}{N_{t}}$: $\lambda=\frac{N_{t+1}}{N_{t}}=\frac{N_{t}}{N_{t}}+\frac{B}{N_{t}}-\frac{D}{N_{t}}=1+b-d$.</p>
<p>All fine when we deal with ideal conditions, where all mother cells divide and there are no mortalities or mutations.</p>
<p>But suppose we're told that only 80% of the mother cells will divide, and the remaining 20% will die without division. In this case: $R_{0}=0.20*0+0.80*2$.</p>
<p>What I'm trying to understand, how will $\lambda$ be affected by this? Does $\lambda$ refers to ideal conditions only, or it depends on the natural situation?</p>
<p>(1) We ignore Immigration and the Emigration at this point.</p>
| [
{
"answer_id": 5407,
"pm_score": 3,
"text": "<p>*It's been several years since I've worked with similar equations. The following reply is based on memory, and if anyone has a firmer grasp of the materials, please modify or answer as you see fit.</p>\n\n<p>I would assume λ is under ideal conditions or as... | [
{
"answer_id": 8564,
"pm_score": 0,
"text": "<p>The same relationship still holds, and $\\lambda$ just describes the finite population growth rate under a particular set of conditions. 'Ideal' conditions (whatever that means) are not implied. Generally you can write: $\\lambda = e^r = R_0^{1/G}$, where ... |
5,430 | <p>In order to survive, prokaryotes such as bacteria need to produce energy from food such as glucose. In eukaryotic cells, respiration is performed by mitochondria, but prokaryotic cells do not have membrane-enclosed organelles. How do prokaryotic cells respirate without mitochondria?</p>
| [
{
"answer_id": 5431,
"pm_score": 5,
"text": "<p>Mitochondria are very similar to bacteria and are thought to have originated from bacteria. This points you to the answer: bacteria produce ATPs the same way mitochondria do, with the oxidation machinery place in their plasma membrane (analogous to the mit... | [
{
"answer_id": 72522,
"pm_score": 0,
"text": "<p>An electrochemical gradient is needed to carry out cellular respiration. Compartimentalization is necessary for gradients to exist. Both mitochondria and certain bacteria possess a double membrane, between which a gradient can be kept. Essentially, they a... |
5,435 | <p>Apparently there're species around as rely heavily on sonar to sense the world around them. </p>
<p>E.g. Bat, Dolphin, Whale ...</p>
<p>The humans, and other terrestrial beings in a lighted world are capable of distinguishing colour in varying degrees of acuity. Is this ability to sense colour in our environment applicable to species (terrestrial, avian, and marine) that rely heavily on sonar? </p>
| [
{
"answer_id": 5440,
"pm_score": 4,
"text": "<p>Any animal using sound cannot sense color though sonar directly, though these animals are not entirely blind and <a href=\"http://www.nhm.ac.uk/nature-online/life/mammals/bats/session3/index.html\" rel=\"noreferrer\">can probably see colors in the infrared... | [
{
"answer_id": 69008,
"pm_score": 1,
"text": "<p>Dolphins, seals and other sea mammals have a monochromatic view, only a green photoreceptor.</p>\n<p><a href=\"http://brain.mpg.de/fileadmin/user_upload/images/Research/Research_Units/Peichl/2001_MPG_whales_and_seals_EN.pdf\" rel=\"nofollow noreferrer\">h... |
5,438 | <p>What's the difference between an appendix and a cecum, and what are their functions?</p>
| [
{
"answer_id": 5439,
"pm_score": 4,
"text": "<p>In herbivores the <strong><em>Cecum</em></strong> is an area that stores plant matter and helps digest it via symbiotic bacteria. Carnivores have smaller Cecums because meat is easier to digest than plant matter. In humans the <strong><em>Cecum</em></stron... | [
{
"answer_id": 73510,
"pm_score": 0,
"text": "<blockquote>\n <p>Appendix and cecum both are parts of the large intestine. </p>\n \n <p>Appendix is the inferior extension of the cecum of the large\n intestine. It is a blind pouch-like structure that resembles a worm,\n hence the name ‘vermiform’.</p... |
5,442 | <p>We know that we wash our hands because germs can get into our body through the nose, the mouth, the eyes, cuts, etc. But I doubt we can completely clean our hands of germs every time we wash them, down to the individual bacterium or virion, even if we use anti-septic soap. So chances are, even if we keep up with our hygiene, germs still get into our body, only in very very small quantities. So here are some questions:</p>
<ol>
<li>In theory, is there a dividing line where we can say "ok, at this non-zero count of bacteria or virion, there is still (<em>an arbitrary probability</em>) that a normal healthy person won't get sick" <strong>for every germ known to man</strong>? If not, are there germs that are known to cause havoc in a healthy person even if he comes into contact with a single individual bacterium or virion?</li>
<li>Do we know a certain trend based on the classification of the germ?</li>
<li>How about the most commonly found germs (whichever they are)?</li>
<li>How about some of the most feared, but not so common, virii known to man, like HIV, ebola, SARS?</li>
</ol>
<p>I think that without being able to answer some of these questions, especially #3, hygiene would be nothing but a ritual activity (because "it just works").</p>
| [
{
"answer_id": 5443,
"pm_score": 4,
"text": "<p>There is a Wikipedia page which gives <a href=\"http://en.wikipedia.org/wiki/Infectious_dose\">some typical values</a> for infectious doses of bacteria. I suspect that lot of these have been taken from <a href=\"http://www.fsis.usda.gov/PDF/Atlanta2010/Sl... | [
{
"answer_id": 6976,
"pm_score": 2,
"text": "<p>Washing your hands is an exercise in probability rather than absolute values. An important thing to keep in mind is that not only is it very hard to kill all the bacteria on your hands, it's also not something you actually want to do. Most of the bacteria... |
5,451 | <p>Can someone explain (or point me to an explanation of) exactly what is meant by all the different symbols I see used for writing genes and proteins?</p>
<p>I think I know that for genes, we use an italic font and for proteins, we use a regular font.</p>
<p>I think I've also learned that for human, all letters are in uppercase (eg. SHH) whereas for mouse, only the first letter is in uppercase and the remaining letters are in lowercase (Shh). (From <a href="http://en.wikipedia.org/wiki/Gene_nomenclature" rel="nofollow">http://en.wikipedia.org/wiki/Gene_nomenclature</a>)</p>
<p>But I'm stumped with all the other "tags" (in quotes because that's how they seem to be used and I don't know how else to think of them) that I see floating around gene and protein symbols.</p>
<p>For example, Myc (MYC?).</p>
<p>I see these three articles in uniprot.org:</p>
<p><a href="http://www.uniprot.org/uniprot/Q99417" rel="nofollow">http://www.uniprot.org/uniprot/Q99417</a> for C-Myc</p>
<p><a href="http://www.uniprot.org/uniprot/P04198" rel="nofollow">http://www.uniprot.org/uniprot/P04198</a> for N-myc</p>
<p><a href="http://www.uniprot.org/uniprot/P12524" rel="nofollow">http://www.uniprot.org/uniprot/P12524</a> for L-Myc</p>
<p>These proteins are all in human, and yet their recommended names are not all caps; what's up with that? But even more confusing to me are the "C-", "N-", and "L-" letters prefixed to them. What in the world are those supposed to be indicating?</p>
<p>Are these all fundamentally different proteins (coded by different genes), but maybe related somehow to each other (thus the common three letters, 'myc' even if they are not all the same case and not all upper case as I thought was supposed to be the case in human), and they are just given these "C-", "N-", and "L-" tags to distinguish one from the other? Does one tag indicate an oncogene or a proto-oncogene? Why do I sometimes see "c-Myc" and other times, "C-Myc"? Does the case of the "C-" mean something? Is there some kind of key or legend I can look at to get answers to all these questions? I've found some explanations in Scott Gilbert's <em>Developmental Biology</em> textbook, but it still doesn't give me all the answers I seek here</p>
<p>I just want to understand how these tags and symbols are being used because it seems to me that when I read research papers (of which I've read many), they are used by different authors in different papers in ways that are not consistent with each other. Either that, or else I'm missing something very basic, which is why I'm asking here.</p>
<p>Thanks in advance for any help.</p>
| [
{
"answer_id": 5454,
"pm_score": 3,
"text": "<p>That's a good question, and honestly, the nomenclature for genes and their coded proteins is somewhat abused in scientific literature. For example, when referring to microbes (like E. coli), gene names are all lowercase (eg, lacZ). The problem of protein n... | [
{
"answer_id": 5456,
"pm_score": 3,
"text": "<p>There is a useful set of links to nomenclature guidelines for all of the main genetic systems at <a href=\"https://en.wikipedia.org/wiki/Gene_nomenclature#Human\" rel=\"nofollow\">this Wikipedia page</a>. Personally, I think that <a href=\"http://instruct.... |
5,484 | <p>During DNA replication, RNA primase puts an RNA primer in the lagging strand. What is the function of this RNA primer? Why can't the enzymes put DNA fragments directly?</p>
| [
{
"answer_id": 5485,
"pm_score": 5,
"text": "<p>DNA polymerases need a primer oligonucleotide (RNA or DNA) - their substrates are an existing 3'-OH group and a dNTP. The primase however is a typical RNA polymerase, capable of initiating polynucleotide synthesis <em>de novo</em> by positioning a compleme... | [
{
"answer_id": 8573,
"pm_score": 3,
"text": "<p>In simple terms:</p>\n\n<p><strong>Function of the RNA primer</strong>: DNA polymerases need a double-stranded DNA region to which they can attach in order to begin copying the rest of the DNA strand. In order to provide this double-stranded attachment sit... |
5,505 | <p>Why is the secondary antibody conjugated to the enzyme in ELISA, instead of the primary antibody? Wouldn't it be easier to conjugate the enzyme to the primary antibody?</p>
| [
{
"answer_id": 5506,
"pm_score": 4,
"text": "<p>Making an antibody-enzyme conjugate isn't trivial. By using a primary/secondary set-up you can use the same well-characterised conjugate in combination with many different primary antibodies (as long as these primaries are all raised in the same species). ... | [
{
"answer_id": 36813,
"pm_score": 1,
"text": "<p>Another reason that secondary antibodies are used is to look for the production of antibodies by a test animal. Follow me for a second with an example that I think will make it clear.</p>\n\n<p><strong>Our Purpose:</strong>\nWe have identified a protein (... |
5,516 | <p>I understand that the atmospheric temperature is sensed relative to external body temperature. However, is the sensation of warmth registered linearly, or is it on a logarithmic scale, similar to sound that works on the Decibel scale? Or is it on another scale entirely?</p>
| [
{
"answer_id": 5625,
"pm_score": 4,
"text": "<p>A more general answer/comment is that technically almost nothing in biology is really linear.</p>\n\n<p>In a linear relation, when one variable increases the other increases proportionally. In biological systems this typically cannot happen because of phys... | [
{
"answer_id": 5619,
"pm_score": 3,
"text": "<p>The human sensation of warmth is not the measurement of static temperature. Humans detect the rate at which heat is leaving (or entering) their body. For instance, if you are sitting in your 0 degree car in the morning, your hand in the open air will fee... |
5,529 | <p>I am confused, can evolution ( speciation ) really occur in such a short time ?</p>
<blockquote>
<p>In 1971, biologists moved five adult pairs of Italian wall lizards from their home island of Pod Kopiste, in the South Adriatic Sea, to the neighboring island of Pod Mrcaru. Now, an international team of researchers has shown that introducing these small, green-backed lizards, <em>Podarcis sicula</em>, to a new environment caused them to undergo rapid and large-scale evolutionary changes."</p>
</blockquote>
<p>Here is a <a href="http://www.youtube.com/watch?v=G7SOPD8cG_M" rel="nofollow noreferrer">short video</a> featuring the scientist.</p>
<p>Two related articles:</p>
<ul>
<li><a href="http://www.sciencedaily.com/releases/2008/04/080417112433.htm" rel="nofollow noreferrer">http://www.sciencedaily.com/releases/2008/04/080417112433.htm</a></li>
<li><a href="http://news.nationalgeographic.com/news/2008/04/080421-lizard-evolution.html" rel="nofollow noreferrer">http://news.nationalgeographic.com/news/2008/04/080421-lizard-evolution.html</a></li>
</ul>
<p><strong>Edit:</strong> I asked a similar question previously about two people having 44 chromosomes and their possibility of creating a new species. You might like to read/answer that as well:</p>
<p><a href="https://biology.stackexchange.com/questions/1051/can-two-humans-with-44-chromosomes-produce-viable-offspring">Can two humans with 44 chromosomes produce viable offspring?</a></p>
| [
{
"answer_id": 5530,
"pm_score": 5,
"text": "<blockquote>\n <p>I am confused, can evolution ( speciation ) really occur in such a short time?</p>\n</blockquote>\n\n<p>Well, <strong>Evolution</strong> and <em>Speciation</em> are not the same. <strong>Evolution</strong> is the adaptation of an existing s... | [
{
"answer_id": 5534,
"pm_score": 3,
"text": "<p><strong>Evolution can occur in just one full generation</strong></p>\n\n<p>Strong selection will rapidly reduce the gene frequencies of genes which cause negatively selected phenotypes. This reduces the likelihood of unfavourable genotypes occurring in the... |
5,536 | <p>When you get sick, you generally don't contract enough bacteria at once for them to succeed in battling your immune system, right? Their numbers must gradually increase in the host's body before they know that they can attack. How does that work?</p>
| [
{
"answer_id": 5539,
"pm_score": 5,
"text": "<p>I think the current answer to this for bacterial infections is <a href=\"http://en.wikipedia.org/wiki/Quorum_sensing\">quorum sensing</a>. Quorum sensing is a signalling pathway in bacteria which senses a molecule that the bacteria themselves secrete. Wh... | [
{
"answer_id": 5538,
"pm_score": 3,
"text": "<p>Infectious agents like bacteria, viruses, fungi, etc., don't <em>know</em> when to \"attack\" or produce pathogenic substances, they just do it under their preferred conditions, and your body's immune system either succeeds in fighting them off immediately... |
5,550 | <p>As I just learned, allelopathy is the action by which plants regulate the growth of other nearby plants. </p>
<p>I have hear of ethylene is a general signal for growth and fruit ripening in particular, but I would like to hear about more specific compounds or proteins that are known to be allelopathic agents and how specific can they be - lots of plants ignore each other and just grow over each other. </p>
<p>@AlanBoyd <a href="https://biology.stackexchange.com/questions/5531/do-plant-plant-interactions-inhibit-growth">has pointed me to a journal</a>, but as its not open content, I'm hoping for a next level review of the mechanisms and actors in this topic...</p>
<p>thanks in advance!</p>
| [
{
"answer_id": 5594,
"pm_score": 3,
"text": "<p>A classic example is juglone from Black Walnut tree roots. This <a href=\"http://pubs.acs.org/doi/pdf/10.1021/ed050p782\" rel=\"nofollow\">review</a> from 1973 discusses juglone and allelopathy, inhibiting growth of other trees. This 1961 <a href=\"http://... | [
{
"answer_id": 5575,
"pm_score": 2,
"text": "<p>As with the massive variety of compounds that serve to protect plants against insect and animals, resulting in a wide range of poisons, antibiotics and other natural insecticides, allelopathic compounds are highly varied with different methods of action: s... |
5,615 | <p>I have a question about the mechanics of human vision which may be as much of a physics question as it is a biology/physiology question. I noticed that if I try to imagine a clear blue daytime sky contrasted with a clear night sky and ask myself which of the two appears closer, my intuition says the daytime sky appears closer. My next thought was, given that a night sky is mostly black, visually the only difference between the two skies is their color. So why is that I want to "blue" is closer than "black"? And if the difference in color is truly what produces the difference in perceived depth, can similar effects be noticed with other color pairs at more familiar distance scales?</p>
<p>But then again, there are a couple of alternative explanations that seem more plausible to me on second thought. A black night sky could just as easily be called a dark sky, and the difference in perceived depth is really more a matter of shading. Then I remembered a night sky has stars of course, and it might be that my mind just wants to place the stars at normal "sky depth", forcing the black backdrop to appear even further away.</p>
<p>(Another related question I've been somewhat curious about: what precisely is the perceived "distance to the sky" as far as our intuitions are concerned?)</p>
| [
{
"answer_id": 5628,
"pm_score": 4,
"text": "<p>Yes, color and shading can certainly affect depth perception, as <a href=\"http://en.wikipedia.org/wiki/Depth_perception\" rel=\"nofollow noreferrer\">explained by wikipedia:</a></p>\n\n<blockquote>\n <p><em>Aerial perspective</em> – Due to light scatteri... | [
{
"answer_id": 28616,
"pm_score": -1,
"text": "<p>I had this same question. I believe the answer is this is a known effect caused by aberrations between your eyes and the way they perceive color. This effect is called Chromostereopsis. I know this is an old topic but hopefully this information will b... |
5,635 | <p>Algal blooms caused by man (harmful algal blooms) are a major ecological problem. An excessive amount of algae causes hypoxia and logically, most marine wildlife can't be sustained in hypoxic conditions. </p>
<p>Can't we use allelopathic plants to reduce the amount of algae significantly?</p>
| [
{
"answer_id": 5744,
"pm_score": 3,
"text": "<p>This has been tried and it sorta works. </p>\n\n<p><a href=\"http://www.skepticalaquarist.com/algae-allelopathy\" rel=\"nofollow\">Algae in general seems to be inhibited by rotting barley straw in the water</a>.<br>\nThere is also an observation (not unive... | [
{
"answer_id": 6818,
"pm_score": 0,
"text": "<p><a href=\"http://qhxb.lib.tsinghua.edu.cn:8080/webpage/environment/chn/upload/Guide1_1.pdf\" rel=\"nofollow\">Here</a> is a good review titled: <em>Use of allelopathy of aquatic macrophytes for algal-bloom control.</em>\n<p>Hu and Hung talked about Macroph... |
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